Signal for packaging of influenza virus vectors

ABSTRACT

The invention provides a packaging (incorporation) signal for influenza virus vectors, and methods of using the signal to transmit and maintain influenza viral and foreign nucleic acid in virus and cells.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a divisional of U.S. patent application Ser. No.10/366,630, filed Feb. 12, 2003, which claims the benefit of the filingdate of U.S. Provisional Application Ser. No. 60/356,538, filed on Feb.13, 2002, and U.S. Provisional Application Ser. No. 60/438,679, filed onJan. 7, 2003, under 35 U.S.C. § 119(e). The disclosure in thoseapplications is incorporated by reference herein.

STATEMENT OF GOVERNMENT RIGHTS

The invention was made, at least in part, with a grant from theGovernment of the United States of America (grant A147446 from theNational Institutes of Health). The government has certain rights in theinvention.

BACKGROUND OF THE INVENTION

The genome of influenza A and B viruses is composed of eightsingle-strand RNA segments of negative polarity, two of which encodeenvelope glycoproteins, hemagglutinin (HA) and neuraminidase (NA).Replication of influenza virus is initiated by the binding of the viralHA proteins on the virion surface to cellular sialic acid containingreceptors. After binding to the receptors, virions are taken into thehost cells by endocytosis. The acidic environment in the late endosometriggers HA conformational changes, initiating fusion between the viralenvelope and the endosomal membrane, and activates the M2 ion channel,resulting in proton influx into the virion interior. Exposure of thevirion interior to low pH is thought to disrupt acid-labile interactionsbetween the M1 protein and ribonucleoprotein complex (RNP), culminatingin the release of RNP into the cytoplasm. The RNP is then transported tothe nucleus, where viral mRNA and the viral genome are synthesized. mRNAenters the cytoplasm and viral proteins are synthesized. Nucleoprotein(NP) enters the nucleus and encapsidates newly synthesized vRNA and,together with the three polymerase subunit proteins (PA, PB1, PB2),forms RNP. In the presence of M1 and NS2 proteins, RNP is exported outof the nucleus. The three plasma membrane-associated proteins (HA, NAand M2) and RNP interact and form new virions by budding. NA isresponsible for viral release from infected cells by removing sialicacids from cellular glycoconjugates and viral glycoproteins (Lamb etal., 2000).

Type A viruses are divided into subtypes based on HA (H1-H15) and NA(N1-N9) antigenicities. In cells infected with two different type Aviruses, intratypic reassortants possessing various combinations of genesegments are produced (Wright et al., 2000). However, intertypicreassortants between type A and B viruses have not been detected innature, although both viruses are cocirculating in human populations.

Investigators have attempted to generate reassortants between type A andB viruses in the laboratory without success (Kaverin et al, 1983;Mikheera et al., 1982; Tobita et al., 1983). Muster et al. (1991)generated a mutant type A virus containing a segment in which thenoncoding regions of a NA segment were replaced with those of thenonstructural (NS) gene of type B virus. Although the mutant virusreplicated more slowly and achieved lower titers than wild-type virus,the generation of such a virus suggested that the noncoding regions ofthe type B NS segment were compatible with influenza virus type Acomponents at the level of RNA transcription and replication. Bycontrast, an RNA segment possessing a foreign coding segment flanked bythe 3′ and 5′ noncoding regions of an influenza A viral RNA segment, wasnot stably maintained in virions after repeated passage (Luytjes et al.,1989). Muster et al. (1991) also disclose that the mutant virus wasattenuated in mice, and that animals infected with the mutant virus wereresistant to challenge with the wild-type virus.

What is needed is a method to identify influenza virus sequences forincorporation and/or maintenance of linked sequence during influenzavirus replication.

SUMMARY OF THE INVENTION

The invention provides an isolated recombinant nucleic acid molecule(polynucleotide), e.g., a vector, comprising incorporation sequences (a“packaging signal” or a vRNA encapsidation signal) for influenza virusand optionally a heterologous nucleic acid segment. Generally,incorporation sequences are present in the about 150 to about 250nucleotides at one or each end of the coding region for each influenzavRNA segment. In one embodiment, influenza virus incorporation sequencescomprise sequences corresponding to the 3′ end of NA vRNA includingsequences corresponding to the N-terminus of the NA coding region, e.g.,37 nucleotides of the 3′ end of type A NA vRNA including 19 nucleotidesof 3′ noncoding sequence and at least nucleotides corresponding to thefirst 19 coding nucleotides for NA and, optionally, incorporationsequences corresponding to the 5′ end of NA vRNA including sequencescorresponding to the C-terminus of the NA coding region, e.g., 67nucleotides of the 5′ end of type A NA vRNA including 28 nucleotides of5′ noncoding sequence and at least 39 nucleotides corresponding to the39 3′ coding nucleotides of NA. In another embodiment, influenza virusincorporation sequences comprise sequences corresponding to the 3′ endof NS vRNA including sequences corresponding to the N-terminus of the NScoding region. In yet another embodiment, influenza virus incorporationsequences comprise sequences corresponding to the 5′ end of HA vRNAincluding sequences corresponding to the C-terminus of the HA codingregion, e.g., 135 nucleotides of the 5′ end of type A HA vRNA including45 nucleotides of 5′ noncoding sequence and at least 80 nucleotidescorresponding to the 80 3′ coding nucleotides of HA and, optionally,incorporation sequences corresponding to the 3′ end of HA vRNA,including sequences corresponding to the N-terminus of the HA codingregion, e.g., 36 nucleotides of the 3′ end of type A HA vRNA including33 nucleotides of 3′ noncoding sequence and at least 3 nucleotidescorresponding to the first 3 coding nucleotides of HA. In a furtherembodiment, influenza virus incorporation sequences comprise sequencescorresponding to the 5′ end of PB2 vRNA including sequencescorresponding to the C-terminus of the PB2 coding region. In anotherembodiment, influenza virus incorporation sequences comprise sequencescorresponding to the 3′ end of M vRNA including sequences correspondingto the N-terminus of the M coding region, e.g., 247 nucleotides of the3′ end of type A M vRNA including 26 nucleotides of 3′ noncodingsequence and 221 nucleotides of sequence corresponding to the N-terminusof the M coding region, and sequences corresponding to the 5′ end of MvRNA including incorporation sequences corresponding to the C-terminusof the M coding region, e.g., 242 nucleotides of the 5′ end of type A MvRNA including 23 nucleotides of 3′ noncoding sequence and 219nucleotides of sequence corresponding to the last 219 nucleotide for theC-terminus of the M coding region. In another embodiment, influenzavirus incorporation sequences comprise sequences corresponding to the 5′end of NS vRNA including sequences corresponding to the N-terminus ofthe NS coding region, e.g., sequences including the 3′ noncodingsequence and at least the first 30 nucleotides corresponding to theN-terminus of the NS coding region, and sequences corresponding to the5′ end of NS vRNA including incorporation sequences corresponding to theC-terminus of the NS coding region, e.g., sequences including the 5′noncoding sequence and at least the last 30 nucleotides of sequencecorresponding to the C-terminus of the NS coding region. In oneembodiment, influenza virus incorporation sequences comprise sequencescorresponding to the 5′ end of PB1 vRNA including sequencescorresponding to the N-terminus of the PB1 coding region and sequencescorresponding to the 5′ end of PB1 vRNA including incorporationsequences corresponding to the C-terminus of the PB1 coding region. Inyet another embodiment, influenza virus incorporation sequences comprisesequences corresponding to the 5′ end of PA vRNA including sequencescorresponding to the N-terminus of the PA coding region and sequencescorresponding to the 5′ end of PA vRNA including incorporation sequencescorresponding to the C-terminus of the PA coding region. Influenza virus“incorporation sequences,” as used herein, are sequences which, whenpresent in vRNA with corresponding (homologous) 3′ and 5′ noncodingregions, result in the incorporation of a nucleic acid moleculecomprising those sequences into virions and the maintenance of thatmolecule in virions during repeated passage.

As described hereinbelow, NA incorporation sequences were identified inmutant viruses with a truncated NA segment using plasmid-based reversegenetics. The NA incorporation sequences were in a region which includedthe 3′ end of NA vRNA, which extended into a portion of the NA codingregion. Thus, this region is useful for packaging and maintenance ofwild-type NA RNA as well as mutant NA RNAs, e.g., RNAs with internaldeletions and/or insertions including recombinant RNAs for expression ofopen reading frames of interest, e.g., a heterologous nucleic acidsegment comprising an open reading frame of interest.

As also described herein, to gain insight into intertypicincompatibility between influenza type A and B viruses, reverse geneticswas employed to generate a reassortant containing an intact type B HAsegment in a type A virus background. However, no virus was produced,despite the fact that the type B HA segment was transcribed by the typeA polymerase complex. Although a type A virus with a chimeric HA segmentcomposed of the entire coding sequence of type B HA flanked by thenoncoding sequence of type A HA was viable, it replicated onlymarginally. A series of type A-based viruses was generated containingchimeric HAs possessing the type A noncoding region together with eitherthe sequence encoding the signal peptide or transmembrane/cytoplasmicregion of type A virus, or both, and the rest of the region derived fromtype B HA. All of these viruses grew to more than 10⁶ tissue cultureinfectious dose₅₀/ml in cell culture, however, the viruses with more ofthe type A HA sequences replicated better, suggesting the role ofprotein-protein interaction or increased HA segment incorporation intovirions in efficient viral growth. All of these A/B chimeric viruseswere attenuated in mice as compared with wild-type A or B viruses.Moreover, all animals intranasally immunized with the chimeric virusessurvived upon challenge with a lethal dose of wild-type type B virus,demonstrating a promising approach for the design of a novel livevaccine virus.

Thus, when an isolated nucleic acid molecule of the invention comprisingincorporation sequences for a particular influenza virus segment, thehomologous 3′ and 5′ noncoding sequences (regions) and a heterologousnucleic acid segment, is introduced to a cell in a vector for vRNAproduction and in the presence of viral proteins and/or viral proteincoding vectors for one or more of PA, PB1, PB2, NP, HA, NA, M, e.g., M1and/or M2, and/or NS, and vRNAs or vectors for vRNA production for oneor more of PA, PB1, PB2, NP, HA, NA, M, e.g., M1 and M2, and/or NS,recombinant virus is produced. The recombinant virus may then be used toinfect a cell. Preferably, vRNA corresponding to a nucleic acid moleculeof the invention is incorporated into virions at an efficiency that isat least 10%, more preferably at least 30%, and even more preferably atleast 50% or more, that of a corresponding wild-type vRNA. In oneembodiment, the nucleic acid molecule includes sequences correspondingto a wild-type vRNA and a heterologous nucleic acid segment, wherein theheterologous nucleic acid segment is introduced to sequences in the vRNAcorresponding to the coding region for that vRNA, which insertionpreferably does not substantially disrupt the incorporation sequences.For instance, the heterologous nucleic acid segment is introduced aftera sequence corresponding to the first 300 nucleotides of the NA codingregion.

In another embodiment, the 3′ NA incorporation sequences correspond tonucleotides 1 to 183, nucleotides 1 to 90, nucleotides 1 to 45,nucleotides 1 to 21, nucleotides 1 to 19 or any integer between 19 and183, of the N-terminal NA coding region, and may include a mutation atthe NA initiation codon. In another embodiment, the 5′ NA incorporationsequences correspond to sequences in the C-terminal coding region of NA,sequences corresponding to the 3′ most 39, 78, or 157, or any integerbetween 1 and 157, nucleotides for C-terminal NA coding region. Inanother embodiment, the 5′ HA incorporation sequences correspond tosequences in the C-terminal coding region of HA, sequences correspondingto the 3′ most 75, 80, 268, 291, or 518, or any integer between 1 and518, nucleotides of the C-terminal HA coding region. The 3′ HAincorporation sequences correspond to nucleotides 1 to 3, 1 to 6, 1 to9, 1 to 15, 1 to 216, 1 to 468, or any integer between 1 and 468, of theN-terminal HA coding region. In one embodiment, the 3′ PB1 incorporationsequences correspond to nucleotides 1 to 250, nucleotides 1 to 200,nucleotides 1 to 150, or any integer between 1 and 250, of theN-terminal PB1 coding region. In one embodiment, the 5′ PB1incorporation sequences correspond to the 3′ most nucleotides, e.g., the3′ 1 to 250 nucleotides, 1 to 200 nucleotides, nucleotides 1 to 150, orany integer between 1 and 250, of the C-terminal PB1 coding region. Inone embodiment, the 3′ PA incorporation sequences correspond tonucleotides 1 to 250, nucleotides 1 to 200, nucleotides 1 to 150, or anyinteger between 1 and 250, of the N-terminal PA coding region. In oneembodiment, the 5′ PA incorporation sequences correspond to the 3′ mostnucleotides, e.g., the 3′ 1 to 250 nucleotides, 1 to 200 nucleotides,nucleotides 1 to 150, or any integer between 1 and 250, of theC-terminal PA coding region. In another embodiment, the 3′ Mincorporation sequences correspond to nucleotides 1 to 250, nucleotides1 to 242, nucleotides 1 to 240, or any integer between 1 and 250, of theN-terminal M coding region, and may include a mutation at the Minitiation codon. In another embodiment, the 5′ M incorporationsequences correspond to sequences in the C-terminal coding region of M,sequences corresponding to the 3′ most 50, 100, or 220, or any integerbetween 1 and 250, nucleotides for C-terminal M coding region. Inanother embodiment, the 3′ NS incorporation sequences correspond tonucleotides 1 to 250, nucleotides 1 to 200, nucleotides 1 to 150,nucleotides 1 to 30, nucleotides 1 to 20 or any integer between 1 and250, of the N-terminal NS coding region, and may include a mutation atthe NS initiation codon. In another embodiment, the 5′ NS incorporationsequences correspond to sequences in the C-terminal coding region of NS,sequences corresponding to the 3′ most 10, 30, 150, 200 or 250, or anyinteger between 1 and 250, nucleotides for the C-terminal NS codingregion.

Accordingly, the invention provides influenza virus vectors whichinclude sequences corresponding to the 3′ and 5′ noncoding regions of aparticular vRNA, incorporation sequences of the corresponding vRNA, anda heterologous nucleic acid segment. Thus, in one embodiment, the vectorincludes the 3′ noncoding region of NA vRNA, 3′ or 5′ NA vRNAincorporation sequences, and optionally both 3′ and 5′ NA incorporationsequences, a heterologous nucleic acid segment, and the 5′ noncodingregion of NA vRNA. In another embodiment, the vector includes the 3′noncoding region of HA vRNA, 5′ or 3′ HA vRNA incorporation sequences orboth 5′ and 3′ HA incorporation sequences, a heterologous nucleic acidsegment, and the 5′ noncoding region of HA vRNA. In another embodiment,the vector includes the 3′ noncoding region of NS vRNA, NS incorporationsequences, a heterologous nucleic acid segment, and the 5′ noncodingregion of NS vRNA. In another embodiment, the vector includes the 3′noncoding region of M vRNA, 5′ or 3′ M incorporation sequences or both5′ and 3′ M incorporation sequences, a heterologous nucleic acidsegment, and the 5′ noncoding region of M vRNA. In yet anotherembodiment, the vector includes the 3′ noncoding region of PB2 vRNA, aheterologous nucleic acid segment, PB2 incorporation sequences, and the5′ noncoding region of PB2 vRNA. When two incorporation sequences areemployed in a vector, they preferably are separated by the heterologousnucleic acid segment. Each vector may be employed so as to prepare vRNAfor introduction to a cell, or to express vRNA in a cell, in which otherinfluenza virus vRNAs and proteins necessary for virus production, arepresent.

In one embodiment, the heterologous nucleic acid segment comprisessequences corresponding to an open reading frame for a marker gene. Inanother embodiment, the heterologous nucleic acid segment comprisessequences corresponding to an open reading frame for a therapeutic gene.In yet a further embodiment, the heterologous nucleic acid segmentcomprises sequences corresponding to an open reading frame for animmunogenic peptide or protein of a pathogen or a tumor cell, e.g., oneuseful to induce a protective immune response. For example, theheterologous nucleic acid segment may encode an immunogenic epitopeuseful in cancer therapy or a vaccine. The vector comprising theheterologous nucleic acid segment may be prepared such thattranscription of vector vRNA results in mRNA encoding a fusion proteinwith an influenza protein such as NA. Thus, it is envisioned that theheterologous nucleic acid segment may be fused with viral incorporationsequences so as to encode a fusion protein, e.g., a fusion with theN-terminal 21 residues of NA. The fusion protein may comprise sequencesfrom two different influenza virus proteins including sequences from twodifferent NA or HA proteins. In another embodiment, the heterologousnucleic acid segment may comprise sequences corresponding to an IRESlinked 5′ to an open reading frame.

To prepare recombinant virus using plasmid-based reverse genetics with aplurality of influenza virus vectors, the influenza virus DNA in avector may be in the sense or antisense orientation relative to thepromoter. Thus, a vector may encode an influenza virus protein (sense),or vRNA (antisense) of an influenza virus A, B, or C, strain or isolate,or a recombinant influenza virus (see Chapters 45 and 46 of FieldsVirology (Fields et al. (eds.), Lippincott-Raven Publ., Philadelphia,Pa. (1996), which are specifically incorporated by reference herein).Any promoter may be employed to express a viral protein and theresulting vector includes a promoter operably linked to a DNA for aparticular influenza virus protein. Preferred promoters for the vectorsencoding vRNA include, but are not limited to, a RNA polymerase Ipromoter, a RNA polymerase II promoter, a RNA polymerase III promoter, aT7 promoter, and a T3 promoter. In one embodiment, the RNA polymerase Ipromoter is a human RNA polymerase I promoter. Preferred transcriptiontermination sequences for the vectors encoding vRNA include, but are notlimited to, a RNA polymerase I transcription termination sequence, a RNApolymerase II transcription termination sequence, or a RNA polymeraseIII transcription termination sequence, or a ribozyme. Thus, a vectorfor vRNA includes a promoter operably linked to a cDNA for an influenzavirus protein in antisense orientation relative to the promoter, whichis operably linked to a transcription termination sequence. To producerecombinant virus with a vector of the invention, certain wild-type vRNAvectors may be omitted and certain wild-type viral protein codingvectors may be replaced. For instance, for a vRNA vector comprising HA3′ and 5′ noncoding sequences, 5′ HA incorporation sequences and aheterologous nucleic acid segment corresponding to a noninfluenza virusprotein coding sequence, e.g., VSV G protein coding sequence, the HAwild-type vRNA vector may be omitted. The vectors of the invention maybe introduced to a cell sequentially or simultaneously. Also provided isa composition comprising a plurality of the above-mentioned vectors, ahost cell contacted with one or more of the vectors, virus prepared bythe method, and a cell infected with the virus.

A plurality of the vectors of the invention may be physically linked oreach vector may be present on an individual plasmid or other, e.g.,linear, nucleic acid delivery vehicle.

Host cells augmented with recombinant DNA molecules as describedhereinabove are useful to prepare infectious replication defectiveinfluenza virus. For example, a host cell stably transformed withrecombinant DNA molecules encoding HA, NA, M1, M2 and NS2 may becontacted with a plurality of vectors, i.e., vectors which express vRNAcomprising PA, vRNA comprising NP, vRNA comprising PB1, vRNA comprisingPB2, and optionally, vRNA comprising a gene of interest; and vectorswhich encode PA, PB1, PB2, and NP.

The methods of producing virus described herein, which do not requirehelper virus infection, are useful in viral mutagenesis studies, and inthe production of vaccines (e.g., for AIDS, influenza, hepatitis B,hepatitis C, rhinovirus, filoviruses, malaria, herpes, and foot andmouth disease) and gene therapy vectors (e.g., for cancer, AIDS,adenosine deaminase, muscular dystrophy, ornithine transcarbamylasedeficiency and central nervous system tumors).

Thus, a recombinant virus for use in medical therapy (e.g., for avaccine or gene therapy) is provided. For example, the inventionprovides a method to immunize an individual against a pathogen, e.g., abacteria, virus, or parasite, or a malignant tumor. The method comprisesadministering to the individual an amount of at least one isolated virusof the invention, optionally in combination with an adjuvant, effectiveto immunize the individual. The virus comprises vRNA comprising apolypeptide encoded by the pathogen or a tumor specific polypeptide.

Also provided is a method to augment or increase the expression of anendogenous protein in a mammal having an indication or diseasecharacterized by a decreased amount or a lack of the endogenous protein.The method comprises administering to the mammal an amount of arecombinant virus of the invention effective to augment or increase theamount of the endogenous protein in the mammal. Preferably, the mammalis a human.

Further provided is a method to inhibit influenza virus infection and/orreplication. The method comprises contacting a cell with a compositioncomprising an isolated nucleic acid molecule comprising influenza virusincorporation sequences for NA, M, HA, NS, NP, PB1, PB2, PA, or anycombination of such molecules, in an amount effective to inhibitinfluenza virus infection and/or replication. The cell may be anuninfected cell or one which is infected with influenza virus. Theincorporation sequences may be specific for one or more types of NA orHA. In one embodiment, the cell is further contacted with a M2 channelinhibitor or a neuraminidase inhibitor.

Also provided is a method to identify an agent which specificallyinhibits or prevents incorporation of influenza virus RNA into virions.The method comprises contacting a cell infected with influenza viruswith an agent; and detecting or determining whether the agentspecifically inhibits or prevents incorporation of influenza virus RNA,such as NA vRNA or recombinant NA vRNA, into virions. Agents identifiedby the method, and uses thereof, e.g., to inhibit or prevent influenzavirus replication, are also provided.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1. Binding of lectin-resistant cell lines. For each cell line,cells were incubated with digoxigenin-labeled Maakia amurensis (MAA) orSambucus nigra (SNA) lectins, followed by fluoresceinisothiocyanate-labeled antidigoxigenin antibody, and then analyzed byFACS. Bold lines, binding of the MAA lectin; narrow lines, binding ofthe SNA lectin; shaded profiles, negative control (no lectin added).

FIG. 2. Structures of the NA genes of the AL3(MaKS)-13 and K4(MaKS)-13mutants. (A) The AL3(MaKS)-13 contains a 936-nucleotide deletion (frombases 220 to 1253) that removes a large portion of the NA gene codingsequence. This mutation also brings a TAG stop codon into frame twobases beyond the deletion, so that the gene encodes only a 66-amino-acidpeptide, corresponding to the cytoplasmic tail, transmembrane region,stalk, and a portion of the head of NA. (B) The K4(MaKS)-13 NA genecontains a 1,066-nucleotide deletion (from bases 130 to 1193) thatremoves a large portion of the NA gene coding sequence. This mutationbrings a TAG stop codon into frame four bases beyond the deletion, sothat the gene encodes only a 38-amino-acid peptide, corresponding to thecytoplasmic tail and transmembrane region of the NA gene.

FIG. 3. Sialidase activity of the parental AM2AL3 and K4 viruses and theAL3(MaKS)-13 and K4(MaKS)-13 mutants. For each sample, virus (5×10² PFU)was incubated in duplicate for 1 hour at 37° C. in the presence of afluorogenic sialidase substrate(4-methylumbelliferyl-α-N-acetylneuraminic acid). The fluorescence ofreleased 4-methylumbelliferone was determined with a fluorometer(Labsystems Fluoroskan II) with excitation at 360 nm and emission at 460nm.

FIG. 4A. Schematic of wild-type and NAFLAG vectors.

FIG. 4B. Schematic of method for NAFLAG virus production.

FIG. 4C. Immunostaining of MDCK cells infected with NAFLAGWT virus orNA(−) virus. The cells were stained with anti-FLAG monoclonal antibody(MAb) M2 or anti-WSN polyclonal antibody.

FIG. 5. Schematic of competition analysis for a recombinant 7 segmentinfluenza virus and NAFLAG virus.

FIG. 6A. Schematic of NAFLAG and NAFLAGM(−) (“−ATG”) vectors.

FIG. 6B. Immunostaining of MDCK cells infected with NAFLAGM(−) virus.The cells were stained with anti-FLAG monoclonal antibody M2 or anti-WSNpolyclonal antibody.

FIG. 7A. In situ hybridization analysis of NAFLAG and NAFLAGM(−)infected cells for FLAG sequence.

FIG. 7B. Replication efficiency of NAFLAGWT virus or NAFLAGM(−) virus.

FIG. 8A. Schematic of NA deletion viruses.

FIG. 8B. Packaging rate of NA deletion viruses.

FIG. 9. Virus titer over time for influenza viruses with 6, 7 or 8segments.

FIG. 10. Schematic showing incorporation signals for influenza viralsegments (stipled).

FIG. 11A. Electron microscope tomography of influenza virions.

FIGS. 11B-F. Color images of rods found by electron microscopetomography of an influenza virion.

FIG. 12. A) Viral segments for a type A influenza virus and a type Avirus whose HA coding sequence is replaced with type B HA. B) Virionsfor a type A influenza virus and a type A virus whose HA coding sequenceis replaced with type B HA.

FIG. 13. Diagram of A/B chimeric HA constructs. Chimeric HA constructswere produced between wild-type A/WSN virus HA (pPolI-WSN-HA) andwild-type B/Lee virus HA (pPolI-B-HA) in a pPolI-based plasmid (pHH21)as described in Neumann et al. (1999).

FIG. 14. Expression of type B HA by A/B HA chimeric viruses. MDCK cellsinfected with each virus were fixed 24 hours post-infection andimmunostained with anti-A/HA, anti-B/HA, or anti-A/NP antibodies.

FIG. 15. Growth properties of A/B HA chimeric viruses. MDCK cells wereinfected with each virus at an MOI of 0.01 TCID₅₀ and monitored forvirus growth. One of two independent experiments with similar results isshown.

FIG. 16. Antibody response to type B virus in mice inoculated with A/BHA chimeric viruses. A) Mice (3 mice/group) were intranasally inoculatedwith each virus (10³ TCID₅₀). Three weeks post-inoculation,nasal/tracheal washes and serum samples were taken from mice and testedfor anti-B virus specific IgA (nasal/tracheal wash) or IgG (serum)antibodies in an ELISA assay. B) HI titers in serum samples were alsotested. Each bar indicates individual mouse infected with the chimericvirus.

FIG. 17. Schematic diagram of mutant HA vRNAs and their efficiency ofvirion incorporation. All mutant HA RNAs are shown in negative-senseorientation. Each mutant contains the GFP open reading frame (insertedin-frame with the HA open reading frame) flanked by a stop codon, 33nucleotides of the 3′ noncoding region and 45 nucleotides of the 5′noncoding region of HA vRNA (black bars). The mutants were designatedaccording to the number of nucleotides derived from the HA codingregions. The HA coding regions are shown as grey bars. The horizontalbroken line indicates a deletion. The lengths of the regions are not toscale. The efficiency of incorporation of mutant HA vRNA into VLPs wasdetermined by dividing the number of cells expressing GFP with that ofcells expressing NP in the VLP-infected cells after fixing cells 16hours postinfection.

FIG. 18. vRNA levels in 293T cells transfected with plasmids expressingmutant HA vRNAs. 293T cells were transfected with pPolIHA(0)GFP(0) orpPolIHA(9)GFP(80) and plasmids expressing PA, PB1, PB2, and NP.

FIG. 19. VSVG(HA)GFP(NA) virus-infected cells express VSV G and GFP.MDCK cells were infected with VSVG(HA)GFP(NA) virus or WSN virus andoverlaid with 1.0% agarose. The infected cells were incubated for 48hours at 37° C., and the plaques were photographed (A, B) under normallight and (C, D) under fluorescent light together with limited normallight to identify plaques. The cells were fixed and permeated with 0.1%Triton-X100 in 3% formaldehyde solution. Viral proteins were detected byimmunostaining with anti-VSV G monoclonal antibody (E, F), anti-HAmonoclonal antibody (Q H), or anti-NP monoclonal antibody (I, J) as theprimary antibody and biotinylated secondary antibody, using theVectastain ABC kit (Vector, Burlingame, Calif.).

FIG. 20. Incorporation of the VSV G protein into VSVG(HA)GFP(NA) virus.Concentrated WNS, VSVG(HA)GFP(NA), and VSV viruses were lysed in asample buffer. Viral proteins were treated with 2-mercaptoethanol,separated by 10% SDS-PAGE, transferred to a PVDF membrane, and incubatedwith anti-VSV G monoclonal antibody or anti-WSN-HA monoclonal antibody.Molecular masses of the marker proteins are shown on the left.

FIG. 21. Growth curves of VSVG(HA)GFP(NA) virus in BHK, CHO, and MDCKcells. BHK (A), CHO (B), and MDCK (C) cells were infected with virus atan MOI of 0.001. At the indicated times after infection, the virus titerin the supernatant was determined using MDCK cells. The values are meansof duplicate experiments.

FIG. 22. Schematic diagram of mutant NS vRNAs and their efficiency ofincorporation.

FIG. 23. Schematic diagram of mutant M vRNAs and their efficiency ofincorporation.

FIG. 24. Schematic of A) viral segments and B) virions expressing twoheterologous proteins.

FIG. 25. Schematic of influenza virus with viral segments for twoheterologous proteins, HIV gp160 and gag.

FIG. 26. Schematic of production of replication incompetent virus usingCre/lox.

DETAILED DESCRIPTION OF THE INVENTION

As used herein, the terms “isolated and/or purified” refer to in vitropreparation, isolation and/or purification of a host cell or virus ofthe invention, so that it is not associated with in vivo substances, oris substantially purified from in vitro substances. As used herein,“substantially pure” means an object species is the predominant speciespresent (i.e., on a molar basis it is more abundant than any otherindividual species in the composition), and preferably a substantiallypurified fraction is a composition wherein the object species comprisesat least about 50 percent (on a molar basis) of all macromolecularspecies present. Generally, a substantially pure composition willcomprise more than about 50 percent, more preferably more than about 80percent of all macromolecular species present in the composition, andeven more preferably more than about 85%, about 90%, about 95%, andabout 99%. Most preferably, the object species is purified to essentialhomogeneity (contaminant species cannot be detected in the compositionby conventional detection methods).

As used herein, the term “recombinant nucleic acid” or “recombinant DNAsequence or segment” refers to a nucleic acid, e.g., to DNA, that hasbeen derived or isolated from a source, that may be subsequentlychemically altered in vitro, so that its sequence is not naturallyoccurring, or corresponds to naturally occurring sequences that are notpositioned as they would be positioned in the native genome. An exampleof DNA “derived” from a source, would be a DNA sequence that isidentified as a useful fragment, or reverse transcribed from RNA, andwhich is then synthesized in essentially pure form. An example of suchDNA “isolated” from a source would be a useful DNA sequence that isexcised or removed from said source by chemical means, e.g., by the useof restriction endonucleases, so that it can be further manipulated,e.g., amplified, for use in the invention, by the methodology of geneticengineering. Recombinant virus is prepared from recombinant nucleicacid.

As used herein, a “heterologous” nucleic acid segment, sequence ormolecule means that the segment, sequence or molecule is derived from asource that is different than a reference nucleic acid segment, sequenceor molecule. For example, a type A influenza virus segment or a portionthereof is heterologous to the corresponding type B influenza virussegment or a portion thereof, a NA viral segment of one influenza strainor serotype is heterologous to a NA viral segment of a different strainor serotype, and a non-influenza virus nucleic acid molecule, e.g., HIVgp160, is heterologous to an influenza virus nucleic acid molecule. Incontrast, a homologous nucleic acid segment is derived from the samesource as a reference nucleic acid segment. Thus, the nucleic acidmolecule of the invention is a chimeric molecule which includes a 3′noncoding region, at least one incorporation sequence and a 5′ noncodingsequence which are homologous to each other.

The phrase “efficient replication” in the context of the presentinvention, is defined as producing high infectivity titers in in vitrotissue culture systems, such as 10⁴-10¹⁰ PFU/ml, and preferably 10⁶-10⁹PFU/ml. The screening of influenza viruses for use in replication orvaccine production, can be assayed using any known and/or suitableassay, as is known in the art. Such assays (alone or in any combination)that are suitable for screening include, but are not limited to, viralreplication, quantitative and/or qualitative measurement of inactivation(e.g., by antisera), transcription, replication, translation, virionincorporation, virulence, HA or NA activity, viral yield, and/ormorphogenesis, using such methods as reverse genetics, reassortment,complementation, and/or infection. For example, virus replication assayscan be used to screen for attenuation or inactivation of the virus. See,e.g., Krug, R. M., ed., The Influenza Viruses, Plenum Press, New York,(1989).

“Sialic acid” refers to a family of amino sugars containing 9 or morecarbon atoms, e.g., N- and O-substituted derivatives of neuraminic acid.

As used herein, “site-specific recombination” is intended to include thefollowing three events: 1) deletion of a target DNA segment flanked bysite-specific recombination sites or sequences, e.g., lox sites; 2)inversion of the nucleotide sequence of a target DNA segment flanked bysite-specific recombination sites or sequences, e.g., lox sites; and 3)reciprocal exchange of target DNA segments proximate to site-specificrecombination sites or sequences, e.g., lox sites located on differentDNA molecules. Site-specific recombinase systems include, but are notlimited to, the Cre/lox system of bacteriophage P1 (U.S. Pat. No.5,658,772), the FLP/FRT system of yeast (Golic and Lindquist, 1989), theGin recombinase of Mu (Maeser et al., 1991), the Pin recombinase of E.coli (Enomoto et al., 1983), and the R/RS system of the pSR1 plasmid(Araki et al., 1992).

Cell Lines and Influenza Viruses That Can Be Used in the PresentInvention

According to the present invention, any cell which supports efficientreplication of influenza virus can be employed in the invention,including mutant cells which express reduced or decreased levels of oneor more sialic acids which are receptors for influenza virus. Virusesobtained by the methods can be made into a reassortant virus.

Preferably, the cells are WHO certified, or certifiable, continuous celllines. The requirements for certifying such cell lines includecharacterization with respect to at least one of genealogy, growthcharacteristics, immunological markers, virus susceptibilitytumorigenicity and storage conditions, as well as by testing in animals,eggs, and cell culture. Such characterization is used to confirm thatthe cells are free from detectable adventitious agents. In somecountries, karyology may also be required. In addition, tumorigenicityis preferably tested in cells that are at the same passage level asthose used for vaccine production. The virus is preferably purified by aprocess that has been shown to give consistent results, before beinginactivated or attenuated for vaccine production (see, e.g., WorldHealth Organization, 1982).

It is preferred to establish a complete characterization of the celllines to be used, so that appropriate tests for purity of the finalproduct can be included. Data that can be used for the characterizationof a cell to be used in the present invention includes (a) informationon its origin, derivation, and passage history; (b) information on itsgrowth and morphological characteristics; (c) results of tests ofadventitious agents; (d) distinguishing features, such as biochemical,immunological, and cytogenetic patterns which allow the cells to beclearly recognized among other cell lines; and (e) results of tests fortumorigenicity. Preferably, the passage level, or population doubling,of the host cell used is as low as possible.

It is preferred that the virus produced in the cell is highly purifiedprior to vaccine or gene therapy formulation. Generally, thepurification procedures will result in the extensive removal of cellularDNA, other cellular components, and adventitious agents. Procedures thatextensively degrade or denature DNA can also be used. See, e.g.,Mizrahi, 1990.

Vaccines

A vaccine of the invention may comprise immunogenic proteins includingglycoproteins of any pathogen, e.g., an immunogenic protein from one ormore bacteria, viruses, yeast or fungi. Thus, in one embodiment, theinfluenza viruses of the invention may be vaccine vectors for influenzavirus or other viral pathogens including but not limited to lentivirusessuch as HIV, hepatitis B virus, hepatitis C virus, herpes viruses suchas CMV or HSV or foot and mouth disease virus.

A complete virion vaccine is concentrated by ultrafiltration and thenpurified by zonal centrifugation or by chromatography. It is inactivatedbefore or after purification using formalin or beta-propiolactone, forinstance.

A subunit vaccine comprises purified glycoproteins. Such a vaccine maybe prepared as follows: using viral suspensions fragmented by treatmentwith detergent, the surface antigens are purified, byultracentrifugation for example. The subunit vaccines thus containmainly HA protein, and also NA. The detergent used may be cationicdetergent for example, such as hexadecyl trimethyl ammonium bromide(Bachmeyer, 1975), an anionic detergent such as ammonium deoxycholate(Layer & Webster, 1976); Webster et al., 1977); or a nonionic detergentsuch as that commercialized under the name TRITON X100. Thehemagglutinin may also be isolated after treatment of the virions with aprotease such as bromelin, then purified by a method such as thatdescribed by Grand and Skehel (1972).

A split vaccine comprises virions which have been subjected to treatmentwith agents that dissolve lipids. A split vaccine can be prepared asfollows: an aqueous suspension of the purified virus obtained as above,inactivated or not, is treated, under stirring, by lipid solvents suchas ethyl ether or chloroform, associated with detergents. Thedissolution of the viral envelope lipids results in fragmentation of theviral particles. The aqueous phase is recuperated containing the splitvaccine, constituted mainly of hemagglutinin and neuraminidase withtheir original lipid environment removed, and the core or itsdegradation products. Then the residual infectious particles areinactivated if this has not already been done.

Inactivated Vaccines. Inactivated influenza virus vaccines of theinvention are provided by inactivating replicated virus of the inventionusing known methods, such as, but not limited to, formalin orβ-propiolactone treatment. Inactivated vaccine types that can be used inthe invention can include whole-virus (WV) vaccines or subvirion (SV)(split) vaccines. The WV vaccine contains intact, inactivated virus,while the SV vaccine contains purified virus disrupted with detergentsthat solubilize the lipid-containing viral envelope, followed bychemical inactivation of residual virus.

In addition, vaccines that can be used include those containing theisolated HA and NA surface proteins, which are referred to as surfaceantigen or subunit vaccines. In general, the responses to SV and surfaceantigen (i.e., purified HA or NA) vaccines are similar. An experimentalinactivated WV vaccine containing an NA antigen immunologically relatedto the epidemic virus and an unrelated HA appears to be less effectivethan conventional vaccines (Ogra et al., 1977). Inactivated vaccinescontaining both relevant surface antigens are preferred.

Live Attenuated Virus Vaccines. Live, attenuated influenza virusvaccines, can also be used for preventing or treating influenza virusinfection, according to known method steps. Attenuation is preferablyachieved in a single step by transfer of attenuated genes from anattenuated donor virus to a replicated isolate or reassorted virusaccording to known methods (see, e.g., Murphy, 1993). Since resistanceto influenza A virus is mediated by the development of an immuneresponse to the HA and NA glycoproteins, the genes coding for thesesurface antigens must come from the reassorted viruses or high growthclinical isolates. The attenuated genes are derived from the attenuatedparent. In this approach, genes that confer attenuation preferably donot code for the HA and NA glycoproteins. Otherwise, these genes couldnot be transferred to reassortants bearing the surface antigens of theclinical virus isolate.

Many donor viruses have been evaluated for their ability to reproduciblyattenuate influenza viruses. As a non-limiting example, the A/AnnArbor(AA)/6/60 (H₂N₂) cold adapted (ca) donor virus can be used forattenuated vaccine production (see, e.g., Edwards, 1994; Murphy, 1993).Additionally, live, attenuated reassortant virus vaccines can begenerated by mating the ca donor virus with a virulent replicated virusof the invention. Reassortant progeny are then selected at 25° C.,(restrictive for replication of virulent virus), in the presence of anH₂N₂ antiserum, which inhibits replication of the viruses bearing thesurface antigens of the attenuated A/AA/6/60 (H₂N₂) ca donor virus.

A large series of H1N1 and H₃N₂ reassortants have been evaluated inhumans and found to be satisfactorily: (a) infectious, (b) attenuatedfor seronegative children and immunologically primed adults, (c)immunogenic and (d) genetically stable. The immunogenicity of the careassortants parallels their level of replication. Thus, the acquisitionof the six transferable genes of the ca donor virus by new wild-typeviruses has reproducibly attenuated these viruses for use in vaccinatingsusceptible adults and children.

Other attenuating mutations can be introduced into influenza virus genesby site-directed mutagenesis to rescue infectious viruses bearing thesemutant genes. Attenuating mutations can be introduced into non-codingregions of the genome, as well as into coding regions. Such attenuatingmutations can also be introduced into genes other than the HA or NA,e.g., the PB2 polymerase gene (Subbarao et al., 1993). Thus, new donorviruses can also be generated bearing attenuating mutations introducedby site-directed mutagenesis, and such new donor viruses can be used inthe reduction of live attenuated reassortants H1N1 and H₃N₂ vaccinecandidates in a manner analogous to that described above for theA/AA/6/60 ca donor virus. Similarly, other known and suitable attenuateddonor strains can be reasserted with influenza virus of the invention toobtain attenuated vaccines suitable for use in the vaccination ofmammals (Ewami et al., 1990; Muster et al., 1991; Subbarao et al.,1993).

It is preferred that such attenuated viruses maintain the genes from thevirus that encode antigenic determinants substantially similar to thoseof the original clinical isolates. This is because the purpose of theattenuated vaccine is to provide substantially the same antigenicity asthe original clinical isolate of the virus, while at the same timelacking infectivity to the degree that the vaccine causes minimal changeof inducing a serious pathogenic condition in the vaccinated mammal.

The virus can thus be attenuated or inactivated, formulated andadministered, according to known methods, as a vaccine to induce animmune response in an animal, e.g., a mammal. Methods are well-known inthe art for determining whether such attenuated or inactivated vaccineshave maintained similar antigenicity to that of the clinical isolate orhigh growth strain derived therefrom. Such known methods include the useof antisera or antibodies to eliminate viruses expressing antigenicdeterminants of the donor virus; chemical selection (e.g., amantadine orrimantidine); HA and NA activity and inhibition; and DNA screening (suchas probe hybridization or PCR) to confirm that donor genes encoding theantigenic determinants (e.g., HA or NA genes) are not present in theattenuated viruses. See, e.g., Robertson et al., 1988; Kilbourne, 1969;Aymard-Henry et al., 1985; Robertson et al., 1992.

Pharmaceutical Compositions

Pharmaceutical compositions of the present invention, suitable forinoculation or for parenteral or oral administration, compriseattenuated or inactivated influenza viruses, optionally furthercomprising sterile aqueous or non-aqueous solutions, suspensions, andemulsions. The compositions can further comprise auxiliary agents orexcipients, as known in the art. See, e.g., Berkow et al., 1987; Goodmanet al., 1990; Avery's Drug Treatment, 1987; Osol, 1980; Katzung, 1992.The composition of the invention is generally presented in the form ofindividual doses (unit doses).

Conventional vaccines generally contain about 0.1 to 200 μg, preferably10 to 15 μg, of hemagglutinin from each of the strains entering intotheir composition. The vaccine forming the main constituent of thevaccine composition of the invention may comprise a virus of type A, Bor C, or any combination thereof, for example, at least two of the threetypes, at least two of different subtypes, at least two of the sametype, at least two of the same subtype, or a different isolate(s) orreassortant(s). Human influenza virus type A includes H1N1, H₂N₂ andH₃N₂ subtypes.

Preparations for parenteral administration include sterile aqueous ornon-aqueous solutions, suspensions, and/or emulsions, which may containauxiliary agents or excipients known in the art. Examples of non-aqueoussolvents are propylene glycol, polyethylene glycol, vegetable oils suchas olive oil, and injectable organic esters such as ethyl oleate.Carriers or occlusive dressings can be used to increase skinpermeability and enhance antigen absorption. Liquid dosage forms fororal administration may generally comprise a liposome solutioncontaining the liquid dosage form. Suitable forms for suspendingliposomes include emulsions, suspensions, solutions, syrups, and elixirscontaining inert diluents commonly used in the art, such as purifiedwater. Besides the inert diluents, such compositions can also includeadjuvants, wetting agents, emulsifying and suspending agents, orsweetening, flavoring, or perfuming agents. See, e.g., Berkow et al.,1992; Goodman et al., 1990; Avery's, 1987; Osol, 1980; and Katzung,1992.

When a composition of the present invention is used for administrationto an individual, it can further comprise salts, buffers, adjuvants, orother substances which are desirable for improving the efficacy of thecomposition. For vaccines, adjuvants, substances which can augment aspecific immune response, can be used. Normally, the adjuvant and thecomposition are mixed prior to presentation to the immune system, orpresented separately, but into the same site of the organism beingimmunized. Examples of materials suitable for use in vaccinecompositions are provided in Osol (1980).

Heterogeneity in a vaccine may be provided by mixing replicatedinfluenza viruses for at least two influenza virus strains, such as 2-50strains or any range or value therein. Influenza A or B virus strainshaving a modern antigenic composition are preferred. According to thepresent invention, vaccines can be provided for variations in a singlestrain of an influenza virus, using techniques known in the art.

A pharmaceutical composition according to the present invention mayfurther or additionally comprise at least one chemotherapeutic compound,for example, for gene therapy, immunosuppressants, anti-inflammatoryagents or immune enhancers, and for vaccines, chemotherapeuticsincluding, but not limited to, gamma globulin, amantadine, guanidine,hydroxybenzimidazole, interferon-α, interferon-β, interferon-γ, tumornecrosis factor-alpha, thiosemicarbarzones, methisazone, rifampin,ribavirin, a pyrimidine analog, a purine analog, foscamet,phosphonoacetic acid, acyclovir, dideoxynucleosides, a proteaseinhibitor, or ganciclovir. See, e.g., Katzung (1992), and the referencescited therein on pages 798-800 and 680-681, respectively.

The composition can also contain variable but small quantities ofendotoxin-free formaldehyde, and preservatives, which have been foundsafe and not contributing to undesirable effects in the organism towhich the composition is administered.

Pharmaceutical Purposes

The administration of the composition (or the antisera that it elicits)may be for either a “prophylactic” or “therapeutic” purpose. Whenprovided prophylactically, the compositions of the inventions which arevaccines, are provided before any symptom of a pathogen infectionbecomes manifest. The prophylactic administration of the compositionserves to prevent or attenuate any subsequent infection. When providedtherapeutically, the attenuated or inactivated viral vaccine is providedupon the detection of a symptom of actual infection. The therapeuticadministration of the compound(s) serves to attenuate any actualinfection. See, e.g., Berkow et al., 1992; Goodman et al., 1990; Avery,1987; and Katzung, 1992.

An attenuated or inactivated vaccine composition of the presentinvention may thus be provided either before the onset of infection (soas to prevent or attenuate an anticipated infection) or after theinitiation of an actual infection.

Similarly, for gene therapy, the composition may be provided before anysymptom of a disorder or disease is manifested or after one or moresymptoms are detected.

A composition is said to be “pharmacologically acceptable” if itsadministration can be tolerated by a recipient patient. Such an agent issaid to be administered in a “therapeutically effective amount” if theamount administered is physiologically significant. A composition of thepresent invention is physiologically significant if its presence resultsin a detectable change in the physiology of a recipient patient, e.g.,enhances at least one primary or secondary humoral or cellular immuneresponse against at least one strain of an infectious influenza virus.

The “protection” provided need not be absolute, i.e., the influenzainfection need not be totally prevented or eradicated, if there is astatistically significant improvement compared with a control populationor set of patients. Protection may be limited to mitigating the severityor rapidity of onset of symptoms of the influenza virus infection.

Pharmaceutical Administration

A composition of the present invention may confer resistance to one ormore pathogens, e.g., one or more influenza virus strains, by eitherpassive immunization or active immunization. In active immunization, aninactivated or attenuated live vaccine composition is administeredprophylactically to a host (e.g., a mammal), and the host's immuneresponse to the administration protects against infection and/ordisease. For passive immunization, the elicited antisera can berecovered and administered to a recipient suspected of having aninfection caused by at least one influenza virus strain.

In a second embodiment, the vaccine is provided to a mammalian female(at or prior to pregnancy or parturition), under conditions of time andamount sufficient to cause the production of an immune response whichserves to protect both the female and the fetus or newborn (via passiveincorporation of the antibodies across the placenta or in the mother'smilk).

The present invention thus includes methods for preventing orattenuating a disorder or disease, e.g., an infection by at least onestrain of pathogen. As used herein, a vaccine is said to prevent orattenuate a disease if its administration results either in the total orpartial attenuation (i.e., suppression) of a symptom or condition of thedisease, or in the total or partial immunity of the individual to thedisease.

At least one inactivated or attenuated influenza virus, or compositionthereof, of the present invention may be administered by any means thatachieve the intended purposes, using a pharmaceutical composition aspreviously described.

For example, administration of such a composition may be by variousparenteral routes such as subcutaneous, intravenous, intradermal,intramuscular, intraperitoneal, intranasal, oral or transdermal routes.Parenteral administration can be by bolus injection or by gradualperfusion over time. A preferred mode of using a pharmaceuticalcomposition of the present invention is by intramuscular or subcutaneousapplication. See, e.g., Berkow et al., 1992; Goodman et al., 1990;Avery, 1987; and Katzung, 1992.

A typical regimen for preventing, suppressing, or treating an influenzavirus related pathology, comprises administration of an effective amountof a vaccine composition as described herein, administered as a singletreatment, or repeated as enhancing or booster dosages, over a period upto and including between one week and about 24 months, or any range orvalue therein.

According to the present invention, an “effective amount” of a vaccinecomposition is one that is sufficient to achieve a desired biologicaleffect. It is understood that the effective dosage will be dependentupon the age, sex, health, and weight of the recipient, kind ofconcurrent treatment, if any, frequency of treatment, and the nature ofthe effect wanted. The ranges of effective doses provided below are notintended to limit the invention and represent preferred dose ranges.However, the most preferred dosage will be tailored to the individualsubject, as is understood and determinable by one of skill in the art.See, e.g., Berkow et al., 1992; Goodman et al., 1990; Avery's, 1987;Ebadi, 1985; and Katsung, 1992.

The dosage of an attenuated virus vaccine for a mammalian (e.g., human)or avian adult organism can be from about 10³-10⁷ plaque forming units(PFU)/kg, or any range or value therein. The dose of inactivated vaccinecan range from about 0.1 to 200, e.g., 50 μg of hemagglutinin protein.However, the dosage should be a safe and effective amount as determinedby conventional methods, using existing vaccines as a starting point.

The dosage of immunoreactive HA in each dose of replicated virus vaccinecan be standardized to contain a suitable amount, e.g., 1-50 μg or anyrange or value therein, or the amount recommended by the U.S. PublicHeath Service (PHS), which is usually 15 μg, per component for olderchildren ≧3 years of age, and 7.5 μg per component for older children <3years of age. The quantity of NA can also be standardized, however, thisglycoprotein can be labile during the processor purification and storage(Kendal et al., 1980; Kerr et al., 1975). Each 0.5-ml dose of vaccinepreferably contains approximately 1-50 billion virus particles, andpreferably 10 billion particles.

The invention will be further described by the following non-limitingexamples.

EXAMPLE 1

Materials and Methods

Viruses and cells. Human H₃N₂ viruses isolated from a single patient,either in embryonated chicken eggs (A/Tottori/AT1/AM2AL3/94; AM1AL3) ofMadin-Darby canine kidney (MDCK) cells (A/Tottori/872/K4/94; K4), wereobtained from T. Ito (Tottori University, Tottori, Japan). Virus stockswere grown either in 10 day-old embryonated chicken eggs (AMZAL3 virus)or on MDCK cells (K4 virus) in minimal essential medium (MEM)supplemented with 0.3% bovine serum albumin and 0.5 mg of trypsin/ml.MDCK cells were maintained in MEM supplemented with 5% newborn calfserum (Sigma, St. Louis, Mo.).

Generation of lectin-resistant cell lines. MDCK cells grown to 75%confluency were washed three times with phosphate-buffered saline andincubated with Maakia amurensis (MAA) lectin (100 mg/ml; BoehringerMannheim, Mannheim, Germany) or Sambucus nigra (SNA) lectin (100 mg/ml;Boehringer Mannheim) in MEM containing 0.3% bovine serum albumin. Aftera 48 hour incubation, the medium was replaced with growth medium (MEM-5%fetal calf serum). Lectin selection was repeated as above two additionaltimes. Surviving cell colonies were then cloned, and the SNA- andMAA-selected cell lines were designated MDCK-Sn10 and MDCK-Ma,respectively.

Fluorometric HPLC method for determination of sialic acid content. Thesialic acid (N-acetylneuraminic acid [NeuAc] and N-glycolylneuraminicacid [NeuGc]) content of both cell lines and the purified virus wasdetermined fluorometrically by high-performance liquid chromatography asdescribed in Suzuki et al. (1997). Each sample was placed in a 5-mlground glass-topped vial and mixed with 100 μl (25 mM) of sulfuric acid.The vials were then heated at 60° C. for 12 hours to hydrolizesialo-sugar chains. After cooling, 50 μl of 1,2-diamino-4,5-methylenedioxybenzene was added to 50 μl of the hydrolyte, and the mixture washeated to 60° C. for 2.5 hours in the dark to develop the fluorescenceof the sialic acid. A 10 μl aliquot of the resulting solution was theninjected into an 880-PU high performance liquid chromatograph (JASCO,Tokyo Japan) equipped with a sample injector valve (model 7125; Reodyne)and a fluorescent spectrophotometer (650-105; Hirachi, Tokyo, Japan)with a 20-μl flow cell and a recorder (Chromatopac C-RSA; Shionadzu,Kyoto, Japan). The fluorescence spectrophotometer was positioned at anexcitation wavelength of 373 nm and an emission wavelength of 448 nm.Standard mixtures (200 pmol/μl) of NeuAc (Sigma) and NeuGc (Sigma) wereused to establish calibration curves.

Fluorometric sialidase activity assay. Virus sialidase activity (5×10⁵PFU was measured with 2′-(4-methylumbelliferyl)-α-D-N-acetylneuraminicacid (Sigma) as a substrate as described in Hara et al. (1987). Brieflythe fluorogenic substrate, dilute 1:2 with 0.5 M sodium acetate (pH4.6), was added to an equal volume of virus samples and incubated for 30minutes at 37° C. Reactions were stopped with 200 ml of 0.5 M Na₂CO₂ (pH10.7), and fluorescence was then incubated at an excitation wavelengthof 360 nm and an emission wavelength of 460 nm. All reactions wereperformed in duplicate.

Sequence analysis of the NA and HA genes. Total viral RNA (vRNA) wasobtained from virus sample with use of the Qiappin vRNA purification kitas instructed by the manufacturer (Qiagen, Inc., Valencia, Calif.). ForcDNA production, the oligonucleotide Uni-12, complementary to theconserved 12 vRNA 3′ terminal nucleotides of influenza A virus genesegments was used as a primer for the Moloney Murine Leukemia Virusreverse transcriptase (Promega, Madison, Wis.) reaction. The NA genecDNA was amplified during 30 rounds of PCR with the NA gene-specificprimers JN2-43 (5′ cRNA sense sequence: 5′-TGGCTCGTTTCTCTCACTATTGCC-3′;SEQ ID NO:1) and JN2-1410r (3′-cRNA antisense sequence:5′-TTATATAGGCATGAGATTGATGTCCG-3′; SEQ ID NO:2) and 10 U of Pwo DNApolymerase (Boehringer Mannheim). The resulting PCR products weresubcloned into the vector pCR21 (Invitrogen, Carlsbad, Calif.) and usedfor automated fluorescent sequencing. The HA gene were cloned in asimilar fashion with the HA gene-specific primers JH3-Up (5′ cRNA senseprimer sequence, 5′-AGCAAAAGCAGGGGATAATTCTATTAACCATGAAGAC-3′; SEQ IDNO:3) and JH3-Down (3′ cRNA antisense primer sequence5′-AGTAGAAACAAGGGTGTTTTTAATTAATGCACTC-3′; SEQ ID NO:4). For eachisolate, three clones were examined to obtain a NA and HA consensussequences.

Results

Generation of lectin-resistant cell lines. To produce cell lines with adecreased level of sialic acid expression on the cell surface, twolectins were used, SNA and MAA, that differ in sialic acid-bindingspecificity. The MAA lectin binds to sialic acid linked to galactose byα(2,3) linkages (Wang et al., 1988), while the SNA lectin is specificfor sialic acids linked to galactose or N-acetylgalactosamine by α(2-6)linkages (Shibuya et al., 1987). The MDCK cell line, which supports thegrowth of influenza viruses, was used as a parent cell for lectinselection. When incubated in the presence of either lectin, the majorityof cells died within a week. Resistant cell clones were then grown outfor stock cultures. The cell lines resulting from MAA and SNA lectinselection were designated MDCK-Ma and MDCK-Sn10, respectively.

Fluorescent-activated cell sorting (FACS) with digoxigenin-labeled MAAand SNA lectins (FIG. 1A) demonstrated high levels of binding of MDCKcells to both lectins, as previously reported (Ito et al., 1997).MDCK-Sn10 cells, selected with α(2,6) linkage-specific lectin, retainedstrong binding to the α(2,3) specific MAA lectin but showed SNA lectinbinding weaker than that of the MDCK parent. By contrast, MDCK-Ma cells,selected with the α(2-3) linkage-specific lectin, bound both lectinsmuch more weakly than MDCK cells.

Viral growth in MDCK-Sn10 and MDCK-Ma cell lines. To learn how influenzaviruses adapt to cells with reduced receptor expression, two influenzavirus variants (AM2AL3 and K4) were chosen with known sialic acidreceptor linkage specificity (Ito et al., 1997). The K4 virusspecifically recognizes NeuAc linked to galactose by α(2-6) linkages[NeuAcα(2-6)Gal], while the AM2AL3 virus is specific for NeuAcα(2-3)Gal.Both viruses replicated almost as well in MDCK-Sn10 cells as in MDCKcells (Table 1). However, the titers of both viruses in MDCK-Ma cellswere 1 log lower than in MDCK cells. Also, after infection with eithervirus, even at a multiplicity of infection of 10, a small percentage ofMDCK-Ma cells continued to grow to confluency without any cytopathiceffects. Virus production could not be detected in these surviving cellsby hemagglutination assay upon replacement of the medium with thatcontaining trypsin, which promotes virus growth. The cells were alsonegative by immunochemical staining for both influenza virus HA and NPproteins (data not shown), thus demonstrating that the cells were notpersistently infected. The surviving cells were designated MaKS. TABLE 1Replication of influenza viruses in lectin-resistant cell lines* Titer(TCID₅₀/ml) Cell line AM2AL3 K4 MDCK 1.8 × 10⁹ 5.6 × 10⁴ MDCK-Sn10 5.6 ×10⁸ 3.2 × 10⁴ MDCK-Ma 1.8 × 10⁸ 5.6 × 10³*The susceptibility of each cell line was determined by infecting cellswith AM2AL3 or K4 with virus and determining the dose required to infect50% of tissue culture cells (TCID₅₀).

FACS analysis with both SNA and MAA lectins demonstrated that the MaKScells, like the MDCK-Ma cells from which they were derived, bound theα(2,6)-specific SNA lectin much more weakly than did MDCK cells (FIG.1B). In addition, the MAA lectin-binding peak of MaKS cells was muchnarrower than that of the MDCK-Ma cell line, with loss of a smallshoulder peak representing a higher MAA-binding population (FIG. 1).

To determine whether reduced amounts of sialic acid were responsible forthe reduced lectin binding of MaKS cells, the sialic acid levels presentin the MaKS cells were quantified by liquid chromatographic analysis.The MaKS cell line showed much lower levels of both NeuAc and NeuGc (8.2and 0.4 pmol/μg of protein, respectively) than MDCK cells (216.0 and 2.5pmol/μg protein), although the NeuGc content was much lower. These datademonstrate an extensive reduction of sialic acid receptor determinantin MaKS cells.

Adaptation of virus in MaKS cells. To determine how AM2AL3 and K4viruses propagate and adapt to growth in cells expressing very lowlevels of virus receptor, both viruses were serially passaged in MaKScells in liquid culture. Since both viruses replicated more poorly inMaKS cells than in MDCK cells (Table 2), passages 1 through 3 wereperformed without dilution, and passages 4 through 13 were performed at1:1,000 dilution. After passage 8, the diameter of plaques produced byeither variant had changed from large (greater than 3 mm) to smaller(approximately 1 nm). By passage 10 and higher, only smaller plaqueswere present when the viruses were assayed with MDCK cells (data notshown). After 13 serial passages, both viruses were able to grow in MaKScells as well as or better than in MDCK cells (Table 2). Virus stocksproduced from either variant after passage 13 were amplified anddesignated AL3(MaKS)-13 and K4(MaKS)-13, respectively. TABLE 2Replication of viruses adapted to growth in lectin-selected cells* Titer(TCID₅₀/ml) AL3(MaKS)- Cell line AM2AL3 13 K4 K4(MaKS)-13 MDCK 1.8 × 10⁹5.6 × 10⁴ 5.6 × 10⁴ 5.6 × 10⁴ MaKS 5.6 × 10⁶ 5.6 × 10⁴ 1.8 × 10³ 1.8 ×10³ Resin, MDCK 321 1 31 0.3 titer/MaKS titer*The susceptibility of each cell line was determined by infecting cellswith AM2AL3 (grown in eggs), K4 (grown in MDCK cells). AL3(MaKS)-13(grown in MaK3 cells), or K4(MaKS)-13 (grown in MaKs cells) stock virusand determining the dose required to infect 50% of tissue culture cells(TCID₅₀). Note that both viruses adapted in MaKS cells grow in thesecells as well as [AL3(MaKS)-13] or better than [K4(MaKS)-13] in MDCKcells,# while the original viruses grow better in MDCK cells.

Mutational analysis of the HA and NA genes of AL3(MaKS)-13 andK4(MaKS)-13 viruses. To determine the molecular basis of virusadaptation to a cellular environment characterized by a reduced receptorconcentration, the HA genes of the AL3(MaKS)-13 and K4(MaKS)-13 viruseswere reverse transcribed, the cDNAs amplified by PCR, and the resultingproducts sequenced. Neither of the genes contained mutations bycomparison with the corresponding HA genes from the two parentalviruses.

Since changes in NA sialidase activity likely influence HAreceptor-binding activity, the NA sequence of the AL3(MaKS)-13 andK4(MaKS)-13 viruses was determined. Sequence analysis of the NA genes ofboth variants revealed large internal deletions (FIG. 2). InAL3(MaKS)-13, the deletion extended from nucleotides 220 to 1253,shifting a reading frame and thus generating a stop codon immediatelyafter the deletion. The coding capacity of this NA is 66 amino acids,corresponding to the cytoplasmic tail, the transmembrane domain, stalkregion, and a short portion of the head region of NA. Similarly, theK4(MaKS)-13 isolate contained a deletion in the NA gene from bases 130to 1193, bringing a stop codon into frame at codon 39. Like theAL3(MaKS)-13 virus, the gene no longer encoded a full catalytic headregion. Thus, viruses passaged in a cell line with very low receptorexpression lost their NA catalytic activity.

To confirm this result, the AL3(MaKS)-13 and K4 (MaKS)-13 variants wereanalyzed for sialidase activity, using a fluorescent sialidase substrate[2′(4-methylumbelliferyl)-α-D-N-acetylneuraminic acid]. Unlike theparental viruses, neither of the NA deletion mutants had detectablesialidase activity (FIG. 3).

Extent of sialylation of viral glycoproteins. During normal infection,viruses with reduced sialidase activity fail to grow efficiently andaggregate at the cell surface (Palese et al., 1974; Shibata et al.,1993). Why, then, do AL3(MaKS)-13 and K4(MaKS)-13 viruses, which lacksialidase activity, grow in MaKS cells? One possible explanation wouldbe that since the sialic acid content of these cells is low, the extentof sialylation of the HA and NA oligosaccharides may also be low,preventing the aggregation of viruses at the infected cell surface, evenwhen viral sialidase activity is absent. To test this hypothesis, thesialic acid content in purified virus preparations was compared betweenAM2AL3 and K4 viruses grown in MDCK cells and AL3(MaKS)-13 virus grownin MaKS cells. The NeuAc content was similar among the virus samples,although the AM2AL3 virus had lower sialic acid content (0.9 pmol ofNeuAc/g of protein) than the other samples (A/Tottori/872/K4/94, 3.8pmol of NeuAc/g of protein; AL3(MaKS)-13, 2.6 pmol of NeuAc/g ofprotein).

Thus, viruses lacking sialidase activity can grow efficiently in cellsexpressing a reduced level of sialic acid because the viralglycoproteins are not sialylated extensively compared with those innormal cell lines and are not bound by the HA, thus preventing viralaggregation.

Discussion

In previous studies, the passage of influenza A viruses in the presenceof an exogenous bacterial sialidase activity and antibodies to the viralNA led to deletion of the viral NA gene (Liu et al., 1993; Liu et al.,1995; Yang et al., 1997). Moreover, NA mutants obtained by suchpassaging were able to grow in cell cultures lacking exogenous sialidaseactivity, as well as in eggs and mice, as a result of compensatorymutations in the HA protein that reduce the molecule's affinity forsialic acid residues (Hughes et al., 2000). As described herein,influenza A viruses can adapt to growth in cells with greatly reducedreceptor expression by large NA gene deletion mutations that abolishsialidase activity. Even though the reduction of viral receptors couldtheoretically affect the receptor-binding HA protein, only the NA genewas altered.

What is the molecular basis of this finding? In normal cellularenvironments where sialic acid receptors are abundant, the loss of NAactivity can be compensated for by reduction of the viral HA affinityfor sialic acid, allowing efficient release of progeny from the hostcell surface and preventing virion aggregation (Hughes et al., 2000). Inthe absence of high levels of viral receptors, as in our MaKS cells, areduction of HA affinity is not necessary to release viral progeny andallow the growth of NA deletion mutants. In fact, high-affinity bindingof the HA protein must be maintained for viral replication in cellsexpressing low levels of viral receptor. Sialidase activity, however, isnot required for virion release and prevention of virion aggregation insuch an environment, since the amounts of sialic acid on cell surfacemolecules are quite low and the sialic acid contents of NA deletionvirions are similar to that of wild-type virions. In fact, sialidaseactivity is likely deleterious for viral growth because it furtherremoves receptor determinant sialic acid from the cell surface.Recently, it was shown that influenza A virus lacking an NA stalk, andthus unable to grow in eggs, acquired a stalk insertion of up to 22amino acids through nonhomologous RNA-RNA recombination (Mitnau et al.,2000). Taken together, these finding indicate that influenza viruses canadapt to new host environments by undergoing radical genetic changes,including large insertions and deletions.

In both this and previous studies (Hughes et al., 2000; Liu et al.,1993), viruses lost sialidase activity by internal deletions in the NAgene segment that spared segment ends encoding the cytoplasmic tail andtransmembrane region. Thus, the preserved regions of the NA gene inthese mutants may be necessary for functions such as virionmorphogenesis and stability.

MaKS cells have a lower sialic acid content than their parental (MDCK)cells. Although similar cell lines have been produced from CHO cells(Ray et al., 1991), they have not proven useful for influenza virusstudies because of their inability to support efficient influenza virus.By contrast, MaKS cells were derived from MDCK cells, a standard cellline in studies of influenza viruses, and should be useful in viralreceptor-based analyses. For example, since exogenously addedgangliosides are known to be incorporated into host cell membranes(Carroll et al., 1985), one could therefore incubate known gangliosideswith MaKS cells and test their ability to serve as viral receptors.

During the past century, three influenza A virus pandemics arose whenthe HA or both the HA and NA genes of emerging viruses were introducedinto a human population. Comparative studies of viruses from differenthost animals suggest that in these pandemic strains, mutations wereintroduced in the HA gene (Bean et al., 1992). Whether similar mutationsare required in the NA to enable the virus to cross host speciesbarriers remains unknown; however, the substrate specificity of thehuman virus N2 NA, which was derived from an avian virus, graduallychanged during its replication in humans (Baum et al., 1991). Resultsdescribed hereinabove indicate that NA mutations can indeed contributeto the ability of influenza A viruses to adapt to new environments. Forexample, a reassortment virus with human virus NA and the remaininggenes from a duck virus failed to replicate in ducks (Hinshaw et al.,1983), even though the NA of the human virus originated from an avianvirus (Scholtissek et al., 1978). This suggests that mutations likelyoccurred in the NA gene during adaptation in humans. Comparative studiesof viral NAs from different animal hosts, in conjunction with recentlydeveloped plasmid-based reverse genetics (Fodor et al., 1999; Neumann etal., 1999), may yield useful insights into how these surfaceglycoproteins contribute to adaptive changes among influenza viruses innature.

EXAMPLE 2

Materials and Methods

Cells. 293T human embryonic kidney cells were maintained in Dulbecco'smedium supplemented with 10% fetal calf serum (FCS) and Madin-Darbycanine kidney (MDCK) cells were maintained in Eagle's mediumsupplemented with 5% newborn calf serum.

Plasmid-based reverse genetics. Influenza A viruses were generated usingplasmids possessing the cDNA of A/WSN/33(H1N1) viral genes under thecontrol of an RNA polymerase I promoter and terminator (referred to asPolI plasmids) and pCAGGS/MCS plasmids expressing influenza viralproteins as described in Neumann et al. (1999) (FIG. 4B). Briefly, PolIplasmids and protein expression plasmids were mixed with a transfectionreagent, Trans IT LT-1 (Panvera, Madison, Wis.), incubated at roomtemperature for 10 minutes, and added to 1×10⁶ 293T cells cultured inOpti-MEM (GIBCO/BRL). Forty-eight hours post-transfection, 0.5 μg per mlof trypsin was added to the medium to activate the HA protein, followedby incubation for 1 hour at 37° C. The supernatant was then collected.

Plasmids. The NAFLAG gene contains the 5′ noncoding region of NA cRNA;51 codons of NA corresponding to the cytoplasmic tail (6 amino acids),transmembrane (29 amino acids) and stalk region (16 amino acids) (FIG.4A); the FLAG epitope (Asp-Tyr-Lys-Asp-Asp-Asp-Asp-Lys; SEQ ID NO:5);two sequential stop codons (TAA TAG; SEQ ID NO:6); and 185 bases of 3′terminus sequence of NA cRNA. This length of 3′ terminus sequence is theshortest found in a truncated NA segment (Yang et al., 1997).pPol1-NAFLAGWT, which produces negative sense NAFLAG RNA, was made bydeleting nucleotides 173 to 1070 (in the positive sense) of the WSN NAgene in pT7Blue-NA (which contains the full-length A/WSN/33 NA geneflanked by BsmB1 sites) and inserting the FLAG sequences, two stopcodons and a StuI site by PCR. This fragment was digested by StuI, andself-ligated. The NAFLAG gene was excised with BsmBI and inserted intothe BsmBI site of pHH21.

pPol1-NAFLAGM(−), for the production of NAFLAGM(−) vRNA, lacks the startcodon for the NA protein. This was achieved by changing the ATGinitiation codon for the truncated NAFLAG protein to GCG by in vitrosite directed mutagenesis system (GeneEditor, Promega).

pPol1NA-(183)GFP(157), which generates RNA containing the 3′ noncodingend of NA vRNA and complementary sequence encoding a fusion protein with61 N-terminal NA codons, enhanced green fluorescent protein (eGFP,Clontech), and 185 bases of the 5′ end of NA vRNA, was produced byreplacing nucleotides 203 to 1109 (in positive sense) of WSN NA gene inpT7Blue-NA with a BglII site by inverted PCR. The eGFP gene was clonedinto this BglII site and StuI site at position 1226 (in the wild-type NAgene) in frame with the NA protein. The NA-(183)GFP(157) gene was theninserted into the BsmBI site of pHH21.

The NA(0)GFP(0) gene, which contains the 3′ noncoding region of NA vRNA,the complementary coding sequence of eGFP, and the 5′ noncoding regionof NA vRNA, was produced by PCR with oligonucleotide primers possessinga BbsI site. This PCR fragment was digested by BbsI and inserted intothe BsmBI site of pHH21 so that upon introduction of the plasmid intocells, RNA containing eGFP coding sequence in negative-sense orientationflanked by 5′ and 3′ noncoding NA vRNA regions, is synthesized.

A series of deletion mutants were produced by PCR mutagenesis. Thedeletion mutants of NA-eGFP fusion protein were made fromNA-(183)GFP(157) gene in pT7blue vector. The NA-(183)GFP(0) gene, whichlacks the entire 3′ terminus (positive sense) of the NA coding region ofNA-(183)GFP(157), was produced by PCR mutagenesis. This mutant containsthe 5′ noncoding region (positive sense), 61 amino acids of NA sequence,the eGFP gene, two stop codons, and the 3′ noncoding region. The PCRmutants, NA-(90)GFP(0), NA-(45)GFP(0), NA-(21)GFP(0) and NA-(18)GFP(0)contain 30, 15, 7, or 6 N-terminal amino acid deletions of the NA codingregion of NA-(183)GFP(0), respectively.

The NA0G185 gene, which contains the 5′ noncoding region, eGFP gene, twostop codons and 185 nucleotides of the 3′ end of NA (positive sense) wasmade in the same manner from NA(61)GFP gene. This mutant has the 5′noncoding region of NA vRNA (28 nucleotides) and 157 nucleotides of NA5′ coding region of vRNA. The NA-(183)GFP(78) and NA-(183)GFP(39)mutants are deletion mutants of NA0G185, which have one-half orone-fourth of the NA 5′ coding region as NA0G185, respectively.

Immunostaining. To detect the FLAG epitope attached to the C-terminus ofthe truncated NA protein, MDCK cells were infected with virus possessingthis epitope and overlayed with 0.6% agarose containing 0.5 μg per ml oftrypsin and 100 μU per ml of Vibrio Cholerae sialidase (GIBCO/BRL). Theinfected cells were fixed with 3% formaldehyde solution, permeated by0.1% Triton-X100 in 3% formaldehyde solution. The FLAG epitope was thendetected using a Vectastain ABC kit (Vector, Burlingame, Calif.) andanti-FLAG monoclonal antibody M2 (Sigma) as the primary antibody andbiotinylated anti-mouse IgG as the secondary antibody. To identify WSNvirus infected cells, a rabbit anti-WSN sera was employed as the primaryantibody.

In situ hybridization. Infected cells were hybridized withdigoxigenin(DIG)-labeled probe and stained using a DIG Nucleic AcidDetection Kit (Roche), according to the manufacturer's protocol. Anoligonucleotide (100 pmol) complementary to the nucleotide sequenceencoding the FLAG epitope (GACTACAAGGACGACGATGACAAG; SEQ ID NO:7) waslabeled by DIG Oligonucleotide Tailing Kit (Roche) at 37° C. for 6hours. Virus-infected cells were fixed with 3% formaldehyde solution,permeated by 0.1% Triton-X 100 in 3% formaldehyde solution andprehybridized at 65° C. for 30 minutes in prehybridization buffer(5×SSC, 1% Blocking Reagent of the Detection Kit, 0.1%N-lauroylsarcosine, 0.02% sodium dodecyl sulfate [SDS]) containing 0.1mg/ml of Poly(A)-DNA of the Detection Kit). Oligonucleotide probes (10pmol) were added to the prehybridization buffer and hybridized at 55° C.for 1 hour. The hybridized cells were washed for 5 minutes with washbuffer (0.1 M maleic acid, 0.15 M NaCl, 0.3% Tween 20, pH 7.5), blockedwith 1% Blocking Reagent for 30 minutes at room temperature, andincubated with anti-DIG antibody (1:500) conjugated with alkalinephosphatase for 30 minutes at room temperature. Cells were then washedwith the wash buffer and incubated with nitroblue tetrazoliumchloride/5-bromo-4-chloro-3-indolyl-phosphate (NBT/BCIP) in thedetection buffer (0.1 M Tris-HCl, 0.1 M NaCl, pH 9.5) at roomtemperature for 3 hours in the dark.

Competitive passages. NAFLAGWT or NAFLAGM(−) virus (300 plaque formingunits [PFU]) was mixed with 3×10⁴ PFU of NA(−) virus and used to infectsubconfluent MDCK cells (multiplicity of infection of 0.01) andincubated for 72 hours in medium containing 0.5 μg per ml of trypsin and100 μU per ml of Vibrio cholerae sialidase. The viruses harvested wereused to infect MDCK cells. This process was repeated 5 times.

Results

An influenza A virus lacking the NA gene segment is viable. Themaintenance of truncated NA gene after repeated passage suggested itsimportance for viral replication. To generate a mutant influenza A viruswithout the NA RNA segment, 293T cells were transfected with plasmidsfor the production of vRNA, with the exception of NA vRNA, and those forthe expression of nine structural proteins. Upon incubation ofsupernatant of the 293T cell culture with MDCK cells in the presence ofVibrio Cholerae sialidase, plaques (189±15.6 μm diameters) wereobserved. In liquid culture, this virus (designated NA(−)) grew up to10⁵ PFU/ml. Thus, an influenza A virus with only 7 vRNA segments wasviable.

A truncated NA segment is required for efficient viral growth. Tounderstand the molecular basis for the stable maintenance of thetruncated NA gene after repeated passage, the growth of virus containinga truncated NA gene was compared to virus lacking the start codon forthe NA gene, coding NA(−) virus. A mutant virus, NAFLAGWT, was generatedby reverse genetics. NAFLAGWT has an NA gene with an internal deletionand a FLAG epitope sequence fused to the truncated NA gene. NAFLAGWTgrew up to 10⁵ PFU/ml and produced plaques in the presence of abacterial sialidase. The plaques were immunostained with anti-FLAGmonoclonal antibody or anti-WSN polyclonal antibody (FIG. 4C). Plaquesproduced by NA(−) or NAFLAGWT virus were stained with anti-WSN antibodybut only those of the latter virus were stained with the anti-FLAGantibody.

To determine the difference in replicative ability, NA(−) and NAFLAGWTviruses were mixed at a ratio of 100:1 and this mixture incubated withMDCK cells (FIG. 5). At 48 hours post-infection, the supernatant wasremoved and used for the production of plaques, which were immunostainedwith anti-FLAG monoclonal antibody. The prevalence of virus with thetruncated NA segment was determined by calculating the percentage ofFLAG-positive plaques among total plaques. This procedure was repeated 4more times. As shown in FIG. 7B, the FLAG-positive plaques in thepopulation gradually increased during passage, reaching nearly 90% bythe fifth passage. This result shows that a virus with 8 segments (eventhough the truncated NA gene does not encode a functional sialidase)grows better than a virus with 7 segments.

Viral RNA is important for efficient viral growth. To determine whethera truncated NA protein or viral RNA is important for efficient viralreplication, a NAFLAGM(−) gene was constructed which lacks both the NAstart codon and another in frame ATG codon (the fifteenth codon) (FIG.6A). Plaques produced by NAFLAGM(−) virus were not detected by anti-FLAGantibody (FIG. 6B), indicating that the protein was not translated. Toensure that NAFLAGM(−) virus possesses the NAFLAGM(−) gene, in situhybridization was performed on plaques produced by this virus using aFLAG sequence-specific probe. These plaques reacted with the probe,confirming the presence of the NAFLAGM(−) gene in this virus. Thereplicative ability of this virus was then compared with the 7 segmentvirus described above. The percentage of plaques labeled with the FLAGsequence-specific probe gradually increased (FIG. 7B), and nearly 80% ofthe plaques became FLAG sequence-positive by the fifth passage (FIG.7A). There were no revertants to those expressing the truncated NAprotein during passage, as demonstrated by the lack of staining withanti-FLAG antibody. Thus, viral RNA itself seems to play an importantrole in efficient viral replication, although the truncated NA proteinmay also play a role in efficient viral replication since the rate atwhich the NAFLAGM(−) became dominant in the mixed infection was slowerthan that of NAFLAGWT virus.

A packaging signal of viral NA RNA extends into the coding sequence.Even after extensive passage of CK2-29 and E17E virus (Hughes et al.,2000), the truncated NA gene was maintained, suggesting that the signalfor vRNA incorporation into virions (i.e., packaging signal) is presentin the coding region of the NA RNA segment. To test this hypothesis, aneGFP coding sequence was inserted into the truncated NA gene in-framewhere the NA sequence was deleted. Thus, this recombinant gene,designated NA-(183)GFP(157), possesses the 3′ noncoding end of NA vRNAand 61 codons of the N-terminal NA coding region, an eGFP coding region,and 185 nucleotides of the 5′ end of NA vRNA. A virus possessing theNA-(183)GFP(157) gene instead of the corresponding wild type NA gene wasprepared and plaque assays performed (FIG. 8A). Over 90% of the plaquesexpressed eGFP indicating that the NA-(183)GFP(157) gene wasincorporated into virions and maintained during viral replication (FIG.8B). This finding was interesting considering that the CAT sequenceflanked by NS noncoding sequences was not maintained for more than 5passages (Luytjes et al., 1989).

Since the difference between the NA-(183)GFP(157) and the CAT constructsis the presence of the viral coding sequence, a gene similar to the CATconstruct was generated, NA(0)GFP(0), that contains eGFP coding sequenceflanked by the 3′ and 5′ NA noncoding regions. This construct lacks theNA coding sequence. Although the virus generated with this gene producedplaques, only a minor population (0.1%) of plaques had one or twoeGFP-expressing cells, indicating that the NA(0)GFP(0) gene was notmaintained in virus during viral replication. In 293T cells transfectedwith plasmids, including one expressing the NA(0)GFP(0) gene for viralproduction, eGFP was expressed at a lesser extent as compared with thosetransfected with the plasmid expressing NA(61)GFP. The amount of PolIplasmid for NA(0)GFP(0) was increased by 10-fold, resulting in a similarnumber of eGFP-expressing 293T cells as cells transfected with PolIplasmid for NA(61)GFP. Even with the 10-fold higher amount of the PolIplasmid for this gene, only 1% of the plaques produced by theNA(0)GFP(0) virus contained eGFP positive cells and only a few cells inthese plaques expressed eGFP. These results indicated that the packagingsignal of viral NA RNA extends into the NA coding sequence.

The role of RNA segments in efficient virion production. To understandwhy a virus with 8 RNA segments grows better than one with 7 segments,infectious virion production was compared among viruses possessing 6, 7,or 8 viral RNA segments (FIG. 9). To produce an 8 segment virus, 293Tcells were transfected with protein expression plasmids for all 9structural proteins and 8 PolI plasmids for normal viral production.Also, a NS PolI plasmid which has two mutations that eliminate NS2production was used; thus, virus produced from 293T cells does notundergo multiple cycles of replication. In addition, HA and NA PolIplasmids were used that have mutations that eliminate production of HAand NA proteins, respectively, so that the effect of the elimination ofgene segments is restricted only to the RNA segment, not the geneproduct. For the production of a 7 segment virus, the PolI plasmid forthe NA gene was eliminated, however, a plasmid for the expression of NAprotein was included. To prepare a virus with 6 segments, the plasmidsfor HA and NA RNAs were omitted, however, plasmids for the expression ofHA and NA proteins were included.

To compare virion production among these viruses, the number ofinfectious virions produced from plasmid-transfected cells was titratedby infecting MDCK cells with these viruses and immunostained infectedcells with anti-WSN antibody 48 hours postinfection. As shown in FIG. 9,the efficiency of infectious virion production was correlated with thenumber of viral RNA segments; the higher the number of viral RNAsegments, the better the virion production. These results indicate therole of viral RNA segments in efficient virion productions.

The 3′ end of NA vRNA is important for its packaging into virions. Tonarrow down the packaging signal in NA vRNA, viruses were prepared thathad truncated NA genes with further deletions in the 3′ or 5′ (vRNAsense) coding region (FIG. 8A). Approximately 40% of plaques produced byNA-(183)GFP(0) virus, which lacks the 5′ terminus of the NA codingregion, expressed eGFP, while only 1.8% of plaques produced by NA0G185virus which lacks the 3′ terminus of NA coding region expressed eGFP.These data indicate that 3′ terminus of the NA vRNA coding region isimportant for virion packaging (FIG. 8).

Discussion

By making deletion constructs, the NA coding region which resulted inthe incorporation of the NA segment into virions was determined. Bothends of the coding regions were found to be important, but the 3′ end ofvRNA corresponding to the 5′ terminus of the NA coding region was moreconsequential than the other end. For the NS segment, the 3′ end of vRNAcorresponding to the 5′ terminus of the NS coding region appears moreimportant than the other end for incorporation (FIG. 22). By contrast,for the HA, M, and NP segments, both ends are important, and for PB2 the5′ end of vRNA corresponding to the 3′ terminus of the PB2 codingregion, is important. These results show that sequences important forvRNA segment incorporation are located in the coding regions, and aretherefore unique to each segment. Possibly, those regions interact withother viral RNAs by base pairing, leading to recruitment of a set of 8vRNA segments into a virion. Since the interaction between vRNA andviral components is virus-specific, that interaction can be a target forthe development of antiviral compounds.

EXAMPLE 3

To obtain a true image of the viral contents, electron microscopytomography was performed (FIG. 11A). An image of virions with a 50 nmthickness was collected. Then, an analysis of one of the virions wasconducted and the 3D images of virion content reconstituted. Thestructures (rods) inside the particle are colored to distinguish eachstructure (FIGS. 11B-F, showing views from the top, side and bottom).Most of the views for the rods are cut, however, for one view, in whichrods were cut across the middle, the entire molecule is shown.Nevertheless, all of the views show inter-rod interactions.

Based on the results summarized above, including data which support thateach viral segment contains a unique sequence that is important forincorporation into virions, which likely contributes to the formation ofthe unique morphologic features of the viral contents, vRNA segments arelikely selectively incorporated into influenza virions. This informationis useful not only to identify targets for developing antiviralcompounds but also for the preparation of attenuated live vaccines asdisruption of virus-specific interactions can inhibit viral replicationand lead to attenuation.

EXAMPLE 4

Materials and Methods

Cells. 293T human embryonic kidney cells and COS-7 cells were maintainedin Dulbecco's modified Eagle's minimal essential medium (DMEM) with 10%fetal calf serum and antibiotics. Madin-Derby canine kidney (MDCK) cellswere grown in MEM with 5% newborn calf serum and antibiotics. Cells weremaintained at 37° C. in 5% CO₂.

Construction of plasmids. The generation of plasmid constructs for viralRNA production (referred as pPolI) containing the HA genes of wild-typeA/WSN/33 (H1N1) (named as pPolI-WSN-HA) and wild-type B/Lee/40(pPolI-B-HA) viruses flanked by human RNA polymerase I promoter andmouse RNA polymerase I terminator was described in Neumann et al.(1999). A series of A/B chimeric HA pPolI constructs were produced byPCR amplification with primers and ProofStart polymerase (QiAGEN) andsubsequent ligation using wild-type HA constructs (FIG. 13). Allconstructs were sequenced to ensure that the unwanted mutations were notincluded.

Biologic assays of HAs expressed in cell culture. Each A/B chimeric HApPolI construct (1 μg) was transfected into COS-7 cells using Trans ITreagent (Mirus) together with the other four pCAGGS-based plasmids (1 μgeach) expressing three polymerase subunits (PA, PB1, and PB2) and thenucleoprotein (NP) of A/WSN virus (Neumann et al., 1991). At 48 hoursafter transfection, cells were treated with Vibrio cholerae sialidase(10 U/ml) and TPCK-trypsin (2.5 μg/ml) at 37° C. for 30 minutes. Cellswere then fixed with 4% paraformaldehyde and immunostained usinganti-B/HA antibody and a commercial ABC detection kit (Vectorlaboratory). Also, hemadsorption assays were performed to assess thereceptor-binding properties of each HA. Briefly, transfected cells wereincubated in a 1% chicken red blood cell suspension in phosphatebuffered saline (PBS) at room temperature for 30 minutes, and thenwashed 5 times before observation. Additionally, fusion assays werecarried out. Briefly, transfected cells were incubated in HEPES buffer(pH 5.0) at 37° C. for 5 minutes followed by incubation in culturemedium for 7 hours. After fixation with cold methanol, fused cells wereimmunostained as described above.

Reverse genetics. Virus was generated by plasmid-based A/WSN or B/Leereverse genetics systems as described in Neumann et al. (1999). Viruseswith wild-type genotypes produced from plasmids were designated asA/WSN-R or B/Lee-R, respectively, and used as controls for comparison.To produce A/B chimeric viruses, chimeric HA PolI-constructs were usedinstead of pPolI-WSN-HA. Viruses produced from 293T cells werebiologically cloned by limiting dilution once and stock viruses wereproduced in MDCK cells.

Experimental infection. To test virus pathogenicity, four-week-oldfemale BALB/c mice, anesthetized with sevoflurane, were infectedintranasally with A/B chimeric or wild-type viruses (10⁵ TCID₅₀/50 μl).Mortality and body weights were monitored for 14 days after infection.Three days after infection, some of the infected mice were euthanizedfor determination of virus titers in organs.

To evaluate the vaccine efficacy of each chimeric virus againstwild-type challenge, mice were intranasally infected with chimeric orwild-type viruses (103 TCID₅₀/50 μl). Three weeks later, a group of micewas euthanized to obtain sera and tracheal-nasal washes for detectingvirus-specific IgA or IgG antibodies. Four weeks after infection, theremaining mice were intranasally challenged under anesthesia with 50LD₅₀ of the wild-type virus (B/Lee-R) and monitored for mortality andbody weight for 14 days.

Detection of virus-specific antibody. Serum and tracheal-nasal washsamples were examined for IgA or IgG antibody by an enzyme-linkedimmunosorbent assay (ELISA) as described in Kida et al. (1982). HIantibodies were also examined using serum samples following treatmentwith receptor-destroying enzyme (RDEII: Denka Seiken).

Results

Construction of A/B chimeric HA genes. To determine the compatibility oftype B HA with type A viral components, a series of chimeric genes wasconstructed between A/WSN and B/Lee HA genes (FIG. 14). Since thenoncoding sequences in both termini of the RNA segments are likelyinterchangeable between type A and B viruses for RNA transcription andreplication (Crescenzo-Chaigne et al., 1999; Desselberger et al., 1980;Muster et al., 1981), a chimeric HA gene was prepared that contains thenoncoding sequences of type A virus and the entire coding sequence fromtype B virus (FIG. 14A, ANBH). This construct would produce intact typeB HA protein. Next, a chimeric gene was prepared in which the signalsequence region of the type B HA coding sequence and the noncodingsequence were changed to that of type A virus (ANSBH). This constructwould also produce intact type B HA after removal of the type A signalpeptide by the cellular signal peptidase. Similarly, a chimeric gene wasprepared in which the sequence encoding transmembrane and cytoplasmicregions of the HA was changed from type B to type A (ANTBH), thusencoding an A/B chimeric HA protein. Another chimeric gene was preparedin which sequences encoding both the signal andtransmembrane/cytoplasmic regions were changed from type B to type A(ANSTBH). This construct would produce the same chimeric HA protein asANTBH after removal of the signal peptide. In addition, a chimera wasprepared that contains all the sequences upstream of the regioncorresponding to the cleavage site from type B and the downstream regionfrom type A virus in the HA coding sequence (ANBW). This construct wouldproduce a chimeric HA protein comprising the HA1 region of type B virusand the HA2 region of type A virus. Finally, a chimeric gene wasprepared in which the signal sequence was changed from type B to type Awithin the ANBW construct, which would result in the same chimeric HAprotein as does ANBW.

Biologic properties of A/B chimeric HAs expressed in cell culture. Toevaluate the functionality of the chimeric HAs, each pPolI HA constructwas transfected into COS-7 cells together with type A virus PA-, PB1-,PB2-, and NP-expressing plasmids. All of the chimeric HA constructs wereexpressed on the cell surface. To test the receptor-binding activitiesof these HAs, hemadsorption assays were performed. Prior to the assay,transfected cells were treated with bacterial sialidase to removeterminal sialic acid in HA oligosaccharide side chains, which wouldinterfere with its receptor-binding activity (Luo et al., 1999). ANBH-,ANSBH-, ANTBH-, and ANSTBH-expressing cells hemadsorbed, while thoseexpressing the other two (ANBW and ANSBW) did not (Table 3). Similarly,the former HAs induced cell fusion, while the latter did not. Theseresults indicated that the former HA chimeras were biologicallyfunctional, whereas the latter two were not, presumably due tostructural alterations. As anticipated from previous reports, functionaltype B HA was produced from intact wild-type B HA segment by type Apolymerase complex and NP (Table 3), confirming the compatibilitybetween type B promoter structures and the type A polymerase complex.TABLE 3 Properties of A/B chimeric HAs expressed in cells and virusespossessing them. Virus titer in Property in cell culture^(a)) Generationof supernatant of Virus titer of Cell surface virus possessingtransfected cell^(b)) the stock^(c)) HA construct expressionHemadsorption Fusion this gene^(b)) (TCID₅₀/ml) (TCID₅₀/ml) Wild-type HAWSN-HA + + + + 3.2 × 10⁷ 6.3 × 10⁷ B-HA + + + − NA^(d)) A/B chimeric HAANBH + + + + 2.0 × 10 6.3 × 10² ANSBH + + + + 1.1 × 10² 2.0 × 10⁶ANTBH + + + + 2.0 × 10⁴ 6.3 × 10⁶ ANSTBH + + + + 1.1 × 10⁶ 3.6 × 10⁶ANBW + − − − NA ANSBW + − − − NA^(a))Each HA construct was transfected in COS-7 cells together with typeA polymerase- and NP-expressing plasmids. At 48 hours post-transfection,biologic properties of each HA was assayed.^(b))Generation of virus possessing the wild-type or chimeric HA genetogether with other influenza A virus genes was performed byplasmid-based reverse genetics system. At 48 hours post-transfection,the supernatant of transfected 294T cells was harvested and titrated forinfectivity.^(c))Virus stock was prepared with MDCK cells. Viruses were harvestedwhen cytopathic effects were advanced.^(d))NA: not available.

Production of viruses with chimeric HAs. To determine whether thechimeric HA genes function during influenza A virus infection, a mutantWSN virus was prepared in which the HA gene was replaced with an A/B HAchimeric gene. Plasmid-based reverse genetics allowed the generation ofwild-type virus with a titer of approximately 10⁷TCID₅₀/ml (Table 3).When pPolI-B-HA was employed instead of pPolI-WSN-HA, no infectiousvirus was generated. The four chimeric HA constructs that werebiologically functional (Table 3) were successfully rescued ininfectious type A virus, albeit to different efficiencies, as judged byvirus titers in the supernatants of plasmid-transfected cells. The viruspossessing the ANBH HA replicated only marginally, while the virus withthe ANSTBH HA was produced at the highest efficiency and grew to morethan 10⁶ TCID₅₀/ml. The other two chimeric HA genes that did not expressbiologically functional proteins did not support viral growth. The A/Bchimeric viruses are designated as ANBH, ANSBH, ANTBH, and ANSTBHviruses.

To confirm that the viruses which were produced indeed contained thetype B HA ectodomain, MDCK cells were infected with these viruses andtested for their reactivity with antibodies to the HA of type A or Bvirus (FIG. 14). Cells infected with viruses containing chimeric HAconstructs reacted with anti-B/HA as well as anti-A/NP antibodies, butnot with anti-A/HA antibody, confirming that these viruses contain typeB HA ectodomains.

Growth characteristics of A/B chimeric viruses in cell culture. Todetermine the replicative properties of the A/B HA chimeric viruses,cells were infected with the viruses at an MOI of 0.01 and the resultingviruses examined for their growth kinetics (FIG. 15). Although none ofthe viruses with the chimeric HAs grew better than wild-type A virus,ANSTBH and ANTBH chimeric viruses grew to nearly 10⁶ TCID₅₀/ml. Unlikeboth type A and B viruses, all of these chimeric viruses formed pinpointplaques, which could be detected only with immunostaining (data notshown).

Replication of the A/B chimeric viruses in mice. The restrictedreplication of the A/B chimeric viruses in cell culture suggested thatthese viruses may be attenuated in vivo. Therefore, mice were inoculatedintranasally with A/B HA chimeric viruses (10⁵ TCID₅₀/50 μl). ANBH viruswas not tested since the titer of the stock was too low (approximately10³ TCID₅₀/ml). None of the other three chimeric viruses tested werelethal to mice, whereas the same dose of the wild-type A virus killedall infected mice while the same dose of the wild-type B virus killedseven of eight infected mice (Table 4). Chimeric viruses were recoveredfrom lungs and nasal turbinates on day 3 post-inoculation, indicatingthat these viruses replicated in mice. Interestingly, replication of thechimeric viruses was more restricted in lungs, and less restricted innasal turbinates, when compared with those of wild-type viruses. Thissuggests a possible link between virus replication level in lung andlethality. Mice infected with ANTBH and ANSTBH chimeric viruses lostweight albeit to a lesser extent as compared with those with wild-type Aviruses. Together, these data indicate that A/B HA chimeric viruses areattenuated in mice. TABLE 4 Pathogenicity of A/B chimeric viruses inmice. Change of Lethality (%) (No. Replication in organs^(b)) bodyweight (%)^(c)) of dead/no. of Virus^(a)) Nasal turbinates Lungs Day 5Day 14 tested) Wild-type virus A/WSN-R 5.0 ± 0.3 8.2 ± 0.1 −27.4 ± 1.1NA^(c)) 100 (8/8)  B/Lee-R 4.7 ± 0.1 5.6 ± 0.1 −19.3 ± 7.9 NA 87.5(7/8)   A/B chimeric virus ANSBH 4.0 ± 0.3 2.8 ± 0.3  2.6 ± 1.0  4.6 ±1.2 0 (0/8) ANTBH 5.3 ± 0.3 4.9 ± 0.1 −17.3 ± 0.7 −8.3 ± 0.4 0 (0/8)ANTSTBH 5.3 ± 0.4 4.6 ± 0.1 −20.9 ± 0.3 −6.2 ± 8.8 0 (0/8) Control(PBS)^(d)) NA NA  2.9 ± 1.3  7.1 ± 0.2 0 (0/8)^(a))Mice were intranasally inoculated with virus (10⁶ TCID₅₀) andmonitored for 14 days. Change of body weight was expressed as mean value± standard deviation (SD (n = 3).^(b))Virus titers were determined in organs at 3 days post-inoculationand expressed as mean value ± SD (n = 3) of log₁₀TCID₅₀/g.^(c))NA: not available.^(d))Control mice were mock-inoculated with phosphate-buffered saline(PBS).

Protection of mice immunized with the A/B HA chimeric viruses uponwild-type virus infection. Since the A/BHA chimeric viruses express anHA ectodomain that is derived from type B virus, it was anticipated thatthese viruses would provide a protective immune response to wild-type Bvirus infection. Prior to challenge experiments, it was determinedwhether anti-B antibodies are elicited in mice following infection withthe chimeric viruses. At three weeks post-inoculation, type Bvirus-specific IgA in nasal/tracheal wash samples and IgG antibodies inserum samples from mice infected with chimeric viruses were detected byan ELISA test (FIG. 16A). HI antibodies were also detected in serumsamples from A/B HA chimeric virus-infected mice (FIG. 16B). Thus,specific antibody responses were demonstrated in all mice infected withthe chimeric viruses, although ANSBH virus elicited a less efficientimmune response.

The chimeric virus-immunized mice were challenged with 50LD₅₀ of thewild-type B virus 4 weeks post-immunization (Table 5). All the micesurvived after challenge, whereas all of the control mock-immunized micedied and only 2 out of 8 mice immunized with WSN virus at a sublethaldose (10³ TCID₅₀) survived upon challenge with wild-type B virus,indicating a specific protective effect of chimeric virus immunizationagainst wild-type B virus infection. In addition, type B virus was notrecovered from nasal turbinates or lungs of mice preimmunized withchimeric viruses, with the exception of one mouse that received ANSBHvirus 3 days post-challenge (data not shown). TABLE 5 Protection of miceimmunized with A/B chimeric viruses against wild-type B virus challengePost-challenge^(b)) Change Survival rate (%) Virus used for of bodyweight (%) (No. of survivors/ immunization^(a)) Day 5 Day 14 no. oftested) Wild-type virus A/WSN-R −17.5 ± 3.6  NA^(c))  25 (2/8) B/Lee-R1.8 ± 0.9 1.4 ± 0.6 100 (8/8) A/B chimeric virus ANSBH −5.6 ± 0.8  −0.7± 0.7  100 (8/8) ANTBH 0.9 ± 0.9 1.9 ± 0.9 100 (8/8) ANSTBH 1.5 ± 0.22.9 ± 0.7 100 (8/8) Control (PBS)^(d)) −20.8 ± 0.5  NA  0 (0/8)^(a))Mice were intranasally infected with each virus listed^(b))Four weeks post-immunization, mice were intranasally challengedwith wild-type B/Lee-R virus (50LD₅₀) and monitored for 14 days afterchallenge. Change of body weight was expressed as mean value ± SD (n =3).^(c))NA: not available^(d))Control mice were mock-immunized with PBS and challenged.Discussion

As described herein, for the first time, an influenza virus wasgenerated which possesses type B, instead of A, HA in the background oftype A virus, thus possessing both type A and B viral proteins. What isessential for the generation of A/B HA chimeric viruses? The chimericgenes must be transcribed and replicated to be maintained in virions.Although conserved among the same virus type, terminal sequences in bothends of the noncoding regions, which contain promoter sequences neededfor RNA transcription and replication (Luytjes et al., 1989), differbetween type A and B RNA segments (Crescenzo-Chaigne et al., 1999;Desselberger et al., 1980). However, a previous study has shown that areporter gene flanked by the noncoding sequence of type B virus NSsegment was transcribed and replicated by a type A polymerase (Muster etal., 1991). Furthermore, a chimeric A/B influenza virus (NA/B-NS)containing a chimeric gene comprising the coding sequence of type Avirus NA and the noncoding sequence of type B virus NS was produced(Muster et al., 1991). These data indicated that the type A polymerasecomplex recognized the promoter sequence of the type B NS gene, albeitto a lesser extent than the homologous promoter of type A virus genes.

The noncoding sequence of each RNA segment includes two structuralregions: terminal sequences that are conserved among all eight RNAsegments and inner segment-specific sequences. Since promoter activityis mainly determined by the former region (Portela et al., 1999), alltype B gene segments are likely be transcribed and replicated by thetype A polymerase complex. In fact, this concept is supported by datashowing that type B HA was expressed in cells cotransfected withpPolI-B-HA containing type B noncoding regions and type A polymerasecomplex- and NP-expressing plasmids (Table 3). Thus, failure to generatea virus containing an intact type B HA segment, i.e., an HA intertypicreassortant, cannot be explained by the lack of RNA transcription andreplication.

The restriction of the generation of the chimeric virus may originate atthe level of RNA segment incorporation into virions; for virusgeneration, the chimeric segment must be packaged into virions. Althoughthe noncoding region of type A NS segment was reported to contain an RNApackaging signal (Luytjes et al., 1989), the packaging mechanism ofinfluenza virus RNA segments has not been fully elucidated. Thesequences or structural features of the RNA segments required for virionincorporation were largely unknown; however, it was recently shown thattype A NA RNA segment possesses its virion incorporation signals at bothends of the coding regions (Fujii et al., 2002 and Example 2). In thisstudy, ANSBH virus replicated more efficiently than ANBH virus (FIG. 14and Table 3). Since the HA proteins expressed in these two virusesshould be identical, the difference in replication efficiency may resultfrom RNA packaging efficiency. That is, a structural feature requiredfor efficient RNA packaging may exist in the region encoding the signalsequence of the HA. Similarly, this may also explain the difference inreplicative efficiency between ANTBH and ANSTBH viruses, which alsoexpress identical HA proteins. In fact, the packaging signals for thetype A HA segment reside at both ends of the coding regions (unpublisheddata). Interestingly, a chimeric NA gene containing the noncodingsequences of type A virus NA and the coding sequence of type B NA wasnot rescued into type A virus (Ghate et al., 1999). This failure may beexplained by lack of a type A NA coding region containing an RNApackaging signal, consistent with the recent finding mentioned above(Fujii et al., 2002).

There may also be critical interactions at the protein level for thegeneration of A/B HA chimeric viruses; chimeric proteins must bepackaged into virions and must be functional for virus replication. Thetype B NA protein supplied in trans can replace the function of a type ANA and be incorporated into type A virions, supporting multiple cyclesof replication of a NA-defective type A virus in cell culture (Ghate etal., 1999). However, as discussed above, a type A virus containing atype B NA was not generated. Although chimeric A/B HA viruses weregenerated, they were attenuated as compared with the wild-type virus.This attenuation may originate from a suboptimal balance betweenreceptor-binding activity of type B HA and the sialidase activity oftype A NA. In addition, replacement of the signal peptide and/ortransmembrane/cytoplasmic domains in the HAs may have altered theirstructure. For example, the transmembrane/cytoplasmic domains in HA mayinteract with other viral components such as M1 leading to efficientvirion assembly (Ali et al., 2000; Cenami et al., 1996; Jin et al.,1997; Zhang et al., 2000). Thus, the inability to generate type A viruspossessing intact type B RNA segments or vice versa may be explained byrestriction at the level of RNA segment incorporation or the level offunctional interaction of proteins or both.

The A/B HA chimeric viruses were attenuated in mice with restrictedreplication in lung and conferred protective immunity to mice againstwild-type B virus infection, suggesting a novel approach for thedevelopment of influenza vaccines. Currently, subcutaneousadministration of trivalent inactivated influenza vaccines is thestandard worldwide, yet their efficacies are suboptimal. This is mainlydue to unsatisfactory induction of mucosal immunity in the upperrespiratory tract where influenza viruses initially invade (Wavening etal., 2001). Thus, these vaccines do not prevent viral infection,although they lessen the severity of the illness. Unlike inactivatedvaccines, live vaccines induce both mucosal and cytotoxic T-cell immuneresponses. The study described herein suggests that chimericmanipulation of the HA gene could control virus attenuation to variousdegrees. Thus, this approach would permit the production of live vaccinestrains with an appropriate balance between attenuation andimmunogenicity. Alternatively, the A/B chimeric HAs can be incorporatedinto cold-adapted influenza A virus whose attenuating mutations arewell-characterized (Maassab et al., 1999). Current cold-adapted vaccinesare mixtures of type A and type B viruses. Potentially, interferencebetween the two viruses affects vaccine efficacy, although this problemhas been addressed by adjustment of the ratio of viral doses. A type Avirus with the A/B chimeric HA would allow the production of liveinfluenza vaccines based on a single attenuated virus rather than twoattenuated viruses, eliminating potential interference between type Aand B viruses.

Thus, in contrast to a live attenuated vaccine having a mixture of typeA and B viruses, with limited information on the attenuating mutationsfor the type B vaccine strain, a virus that contains type B HA and NA inthe background of type A virus can be produced. This approach allows theproduction of vaccines based on a master vaccine strain withwell-defined attenuating mutations for the expression of type A as wellas type B HA and NA. Moreover, knowledge of the packaging signals forviral segments also promotes development of improved live attenuatedinfluenza vaccines.

EXAMPLE 5

Materials and Methods

Cells and virus. 293T human embryonic kidney cells (a derivative of the293 line into which the gene for simian virus 40 T antigen was inserted)were maintained in Dulbecco's modified Eagle medium supplemented with10% fetal calf serum (FCS). For baby hamster kidney (BHK), Chinesehamster ovary (CHO), and Madin-Darby canine kidney (MDCK) cells, DMEMcontaining 5% FCS and MEM containing 10% and 5% newborn calf serum wereused, respectively. All cells were maintained at 37° C. in 5% CO₂.A/WSN/33 (H1N1) (WSN) virus was generated by reverse genetics asdescribed in Neumann et al. (1999) and propagated in MDCK cells. VSVIndiana strain generated by reverse genetics was propagated in BHKcells.

Reverse genetics. For generation of influenza virus-like particles(VLPs) and mutant influenza A viruses, plasmids possessing the cDNA ofWSN viral genes under the control of the human RNA polymerase I promoterand the mouse RNA polymerase I terminator (referred to as PolI plasmids)and the eukaryotic protein expression vector pCAGGS/MCS (controlled bythe chicken P-actin promoter) were used. Briefly, PolI plasmids andprotein expression plasmids were mixed with a transfection reagent,Trans IT LT-1 (Panvera, Madison, Wis.), incubated at room temperaturefor 15 minutes, and added to 1×10⁶ 293T cells cultured in Opti-MEM I(GIBCO/BRL). Six hours later, the DNA-transfection reagent mixture wasreplaced with Opti-MEM I containing 0.3% BSA and 0.01% FCS. Forty-eighthours later, VLPs or mutant influenza A viruses in the supernatant wereharvested. Transfectants generated in this study all contain a mutant HAvRNA segment together with other vRNA segments of WSN virus and aredesignated by the name of the mutant HA vRNA segment (e.g., a VLPcontaining the HA(0)GFP(0)RNA segment is designated the HA(0)GFP(0)VLP).

Construction of plasmids. pPolIHA(0)GFP(0) was used to producenegative-sense RNA containing the 3′ noncoding region of HA vRNA, thecomplementary coding sequence of enhanced green fluorescent protein(GFP, Clontech), and the 5′ noncoding region of HA vRNA. Briefly, theGFP gene was amplified by PCR with primers containing the BsmBI sitesand the 3′ or 5′ noncoding sequence of HA, digested with BsmBI, andcloned into the BsmBI site of the PolI plasmid. Introduction of thisplasmid into cells results in an RNA containing the GFP-coding sequencein negative-sense orientation flanked by 5′ and 3′ noncoding regions HAvRNA.

pPolIHA(468)GFP(513) was made as follows: pPolIHA for the production ofWSN vRNA was first amplified by inverse PCR using back-to-back primersBam500R (5′-GCGGATCCTCCCCTATGGGAGCATGATAC-3′; SEQ ID NO:6) and XbaI218F(5′-GCTCTAGAAACTCTGTTATCGAGAAAATG-3′; SEQ ID NO:7). The PCR product wasdigested with BamHI and XbaI, and then the GFP gene was cloned into theBamHI site and XbaI site. The resultant plasmid, pPolIHA(468)GFP(513),was used for the production of negative-sense RNA, containing the 3′noncoding region and 468 bases of the 3′ coding region of HA vRNA, theGFP coding sequence, 513 bases of the 5′ coding region and the 5′noncoding region of HA vRNA. A series of HA deletion mutants was alsoproduced by inverse PCR in the same manner. The mutants were designatedaccording to the number of nucleotides derived from the HA codingregion, e.g., the HA(9)GFP(80) RNA segment contains the 3′ HA noncodingregion, 9 nucleotides from the HA coding sequence corresponding to theN-terminal region, GFP open reading frame, 80 nucleotides from the HAcoding sequence corresponding to the C-terminal region, and the 5′ HAnoncoding sequence. All plasmid constructs were sequenced to ensure thatunwanted mutations were not introduced by PCR.

pPolIHA(0)VSVG(0), which was used to produce negative-sense RNAcontaining the 3′ noncoding region of HA vRNA, the complementary codingsequence of V SVG, and the 5′ noncoding region of HA vRNA, was producedby PCR. Briefly, the VSV G gene was amplified by PCR using pCAGGS-VSVGas a template and primers containing the BsmBI sites and the 3′ or 5′noncoding sequence of HA. The PCR product was then digested with BsmBI,and cloned into the BsmBI site of the pHH21 vector. pPolIHA(9)VSVG(80)was made by cloning the coding sequences of VSV G into the BamHI siteand the XbaI site of pPolIHA(9)GFP(80). pPolINA(183)GFP(157), whichcontains the 3′ noncoding ends of NA vRNA and a complementary sequenceencoding a fusion protein possessing 61 N-terminal NA codons and GFP,two consecutive stop codons (TAA-TAG), and 185 bases of the 5′ end of NAvRNA, was produced as follows. The region corresponding to nucleotides203 to 1109 (positive sense) of WSN NA gene in pT7Blue-NA was firstreplaced with a BglII site by inverse PCR. The GFP gene was then clonedinto this BglII site and StuI site at position 1226 (in the wild-type NAgene) in frame with the NA protein. The NA(183)GFP(157) gene was theninserted into the BsmBI site of a PolI plasmid, pHH21.

pPolINA(183)GFP(157)Met(−), used for the production of negative-senseNA(183)GFP(157)Met(−) RNA, which lacks the start codon for the NAprotein, was generated as follows. The ATG initiation codon and anotherATG at the fifteenth codon of the NA(183)GFP(157) gene inpPolINA(183)GFP(157) was change to GCG by in vitro site directedmutagenesis (GeneEditor, Promega). The resultant construct,pPolINA(183)GFP(157)Met(−), contains the 3′ NA noncoding region (19nucleotides), 183 nucleotides corresponding to the N-terminal NA codingregion, the GFP open reading frame, two consecutive stop codons(TAA-TAG), 157 nucleotides corresponding to the C-terminal NA codingregion, and the 5′ NA noncoding region (28 nucleotides), under thecontrol of the human RNA polymerase I promoter and the mouse RNApolymerase I terminator.

Immunostaining assay. Sixteen hours after infection with influenza VLPs,cells were washed twice with phosphate-buffered saline (PBS) and fixedwith 3.7% formaldehyde (in PBS) for 20 minutes at room temperature,followed by treatment with 0.1% TritonX-100 and processed. To examinethe efficiency of VLP generation, 10⁶ cells were incubated with 0.1 mlof the culture supernatant of plasmid-transfected 293T cells and thenumber of NP-positive cells, as detected by the immunostaining assay,was recorded at 16 hours post-infection.

Western blotting. The VLPs or mutant viruses were spun down for 1.5hours at 50,000×g at 4° C. Concentrated VLPs or viruses were resuspendedin lysis buffer (0.6 M KCl, 50 mM Tris-HCl, pH 7.5, 0.5% Triton X-100).The lysates were placed on 15% SDS-polyacrylamide gels,electrotransferred to a polyvinylidene difluoride (PVDF) membrane,blocked overnight at 4° C. with 5% skim milk in PBS, and incubated withanti-WSN virus polyclonal antibody, anti-HA monoclonal antibody, oranti-VSVG monoclonal antibody for 1 hour at room temperature. Themembrane was washed three times with PBS containing 0.05% Tween-20.Bound antibodies were detected with a VECTASTAIN ABC kit (Vector) andKonica immunostaining kit (Konica).

Northern hybridization. vRNA present in 293T cells transfected with PolIplasmids was extracted with the Isogen RNA extraction kit (Nippon Gene,Tokyo, Japan) at 24 hour post-transfection. RNAs were glyoxalated inglyoxal/DMSO/phosphate buffer at 50° C. for 1 hour and separated byelectrophoresis on 1.0% agarose gel in 10 mM phosphate buffer (pH 7.0).RNAs were blotted onto nylon membrane and hybridized with anoligonucleotide probe complementary to the GFP sequence(ATGGCCGACAAGCAGAAGAACGGCATCAAGG; SEQ ID NO:8) (10 pmol), which waslabeled using a DIG Oligonucleotide Tailing Kit (Roche) at 37° C. for 30minutes. Hybridization was done using the GFP probe in Easy Hyb (Roche)overnight at 42° C. The RNA bands were detected by using DIG NucleicAcid Detection Kit (Roche). Briefly, the hybridized membrane was washedwith a wash buffer (0.1 M maleic acid, 0.15 M NaCl, 0.3% Tween20, pH7.5), blocked with 1% Blocking Reagent for 30 minutes at roomtemperature, and incubated with anti-DIG antibody (1:5000) conjugatedwith alkaline phosphatase for 30 minutes at room temperature. Themembrane was then washed with the wash buffer and incubated withnitroblue tetrazolium chloride/5-bromo-4-chloro-3-indolyl-phosphate(NBT/BCIP) in the detection buffer (0.1 M Tris-HCl, 0.1 M NaCl, pH 9.5)at room temperature in the dark. The RNA bands were detected by usingDIG Nucleic Acid Detection Kit (Roche). Control RNA was extracted frommock-transfected 293T cells.

Replicative properties of transfectant viruses. BHK, CHO, or MDCK cellsin duplicate wells of 24-well plates were infected with a virus,overlaid with MEM medium containing 0.01% FCS, and incubated at 37° C.At different times, supernatants were assayed for infectious virus inplaque assays on MDCK cells.

Results

The coding region of HA vRNA was required for the incorporation of theHA segment into virions. To determine whether the coding regions of HAvRNA are needed for its virion incorporation as for NA vRNA, twoplasmids were constructed: pPolIHA(0)GFP(0) containing only the 3′ and5′ noncoding regions of HA vRNA and the GFP coding sequence, andpPolIHA(468)GFP(513) in which the GFP coding sequence was inserted intothe HA gene in-frame after deleting the HA sequence at nucleotidepositions 500-1218 (in positive sense orientation) (FIG. 17). The latterconstruct possesses the 3′ HA noncoding region (33 nucleotides), 468nucleotides corresponding to the N-terminal coding region, the GFP openreading frame with a stop codon, 513 nucleotides corresponding to theC-terminal HA coding region, and the 5′ HA noncoding region (45nucleotides). The resultant fusion protein contains the N-terminal 156amino acids of the HA and the entire GFP sequence.

To generate VLPs possessing these mutant HA vRNAs, 293T cells weretransfected with pPolIHA(0)GFP(0) or pPolIHA(468)GFP(513), and 7 RNAPolI plasmids for the production of the remaining influenza viral RNAsegments and protein expression plasmids for nine viral proteins (i.e.,PA, PB1, PB2, NP, HA, NA, M1, M2, and NS2). Forty-eight hourspost-transfection, VLPs in the supernatants of 293T cell cultures wereharvested and used to infect MDCK cells. Since the resultant VLPspossessed mutant HA, they expressed GFP and all viral proteins exceptHA. Consequently, no infectious progeny virus was generated (data notshown). The efficiency of virion incorporation of mutant HA vRNA wasdetermined by dividing the number of cells expressing GFP (i.e., thenumber of VLPs that possessed the segment encoding GFP gene) with thatof cells expressing NP (i.e., the number of all infectious VLPs) at 16hours post-infection. The titer of all infectious VLPs in the culturesupernatant of 293T cells transfected with pPolIHA(468)GFP(513) (i.e.,the number of NP-positive cells) was 7.4×10⁵ infectious VLPs/ml and thetiter of VLPs containing HA(468)GFP(513) RNA (i.e., the number ofGFP-positive cells) was 3.2×10⁵ VLPs/ml. These results indicated that42.8% of all infectious VLPs generated harbored mutant HA vRNA (FIG.18). By contrast, only 3.9% of VLPs possessed the HA(0)GFP(0)RNA segment(FIG. 18). These results suggested that the coding regions of HA vRNAare required for the incorporation of HA segment into influenza virions.

Both the 3′ and 5′ ends of the coding region of HA vRNA are importantfor the incorporation of HA segment into virions. Previously, it wasshown that the 3′ end of the NA vRNA coding region plays a more crucialrole in virion incorporation than does the 5′ end. Thus, it wasdetermined whether the 3′, 5′, or both ends were important for virionincorporation of the HA vRNA segment. To address this issue, theHA(0)GFP(1011) gene was prepared, which lacked the 3′ terminus of the HAvRNA coding region, and the HA(966)GFP(0) gene, which lacked the 5′terminus of the HA vRNA coding region (FIG. 17), and virionincorporation of these HA vRNAs examined as described above. Althoughthe amounts of both vRNAs in plasmid-transfected cells were comparableto that of HA(468)GFP(513) vRNA (data not shown), the efficiency ofsegment incorporation of both HA(0)GFP(1011) and HA(966)GFP(0) was only6.8% and 8.4%, respectively (FIG. 17), indicating that both the 3′ and5′ termini of the HA vRNA coding region played an important role invirion incorporation of HA segment.

To further define the critical region in HA vRNA for its incorporationinto virions, a series of VLPs were generated, which possess truncatedHA vRNAs with further deletion in the 3′ and/or 5′ coding region (FIG.17). The incorporation efficiency of mutant HA vRNA into VLPs was thendetermined. Since further deletion in the 3′ end leaving only 15nucleotides and the 5′ end leaving 268 nucleotides did not affect theefficiency of HA vRNA incorporation (compare HA(468)GFP(513) withHA(15)GFP(268)), additional deletion constructs were prepared usingpPolIHA(15)GFP(268), which possesses 15 nucleotides of the 3′ end and268 nucleotides of the 5′ end of the HA coding region. Although theextent of vRNA incorporation was reduced gradually as the extent ofdeletions increased, 80 nucleotides in the 5′ HA coding region seemedminimally required for efficient virion incorporation of HA vRNA(compare HA(15)GFP(80) with HA(15)GFP(75)). Further deletion analysisdemonstrated that HA(9)GFP(80) leaving 9 nucleotide residues of the HAcoding region at the 3′ end resulted in efficient virion incorporationof HA vRNA (more than 65%), although the level of HA(9)GFP(80) vRNApresent in transfected cells did not appreciably differ from that ofHA(0)GFP(0) vRNA (FIGS. 17 and 18). These results indicate that 9nucleotides in the 3′ end and 80 nucleotides in the 5′ end of the HAcoding region are required for efficient HA vRNA incorporation intovirions.

Generation of a novel influenza A virus whose HA and NA genes containthe coding sequences of foreign genes. Since the sequences required forHA segment incorporation into virions had been determined, it wasexamined whether a foreign gene flanked by those sequences could beincorporated into influenza A viruses and maintained during repeatedpassage. As a model foreign gene, the VSV G coding sequence was insertedinto the BamHI and XbaI sites of pPolIHA(9)GFP(80) instead of GFPsequence. The resultant construct was designated pPolIHA(9)VSVG(80),possessing the 3′ HA noncoding region (33 nucleotides), 9 nucleotidescorresponding to the N-terminal HA coding region, the VSV G open readingframe with a stop codon (1552 nucleotides), 80 nucleotides correspondingto the C-terminal HA coding region, and the 5′ HA noncoding region (45nucleotides). As a control, a vector was constructed, pPolIHA(0)VSVG(0),which possesses only the 3′ and 5′ noncoding regions, but not the codingregion of HA vRNA. Since VSV G protein should substitute for both HA andNA proteins, the NA coding region can be substituted with a foreigngene. Therefore, pPolINA(183)GFP(157)Met(−) was constructed forproduction of a recombinant NA RNA segment containing the GFP codingsequence and the NA coding sequences required for the efficient virionincorporation of NA segment. In this construct, the initiation codon forthe NA open reading frame was destroyed by substituting ATG to GCG Thus,the GFP open reading would be translated from its own initiation codon.

293T cells were transfected with plasmids for the production of bothrecombinant HA(9)VSVG(80) and NA(183)GFP(157)Met(−) segments and theremaining 6 viral RNA segments, as well as plasmids for the expressionof influenza virus polymerase proteins, NP, M1, M2, NS2, and VSV G. At72 hours after transfection, the supernatants of 293T cells wereharvested and plaque assays performed using MDCK cells. A transfectantvirus harboring HA(9)VSVG(80) RNA segment and NA(183)GFP(157)Met(−) RNAsegment (designated VSVG(HA)GFP(NA) virus) was viable and producedplaques expressing GFP in the absence of trypsin (FIG. 19).Immunostaining confirmed the expression of VSV G, but not HA, containingplaques (FIG. 19). Cells infected with VSVG(HA)GFP(NA) virus, but notcontrol WSN virus, also expressed GFP. By contrast, no plaques wereobserved when pPolIHA(0)VSVG(0) plasmid was used instead ofpPolIHA(9)VSVG(80), although single cells expressing GFP and/or NPprotein were detected in MDCK cells (data not shown). Moreover, it wasobserved that both VSVG and GFP continued to be expressed in MDCK cellsinfected with the VSVG(HA)GFP(NA) virus after five consecutive passages(data not shown). No mutation was detected in the remaining HA region ofthe HA(9)VSVG(80) RNA segment of VSVG(HA)GFP(NA) virus after fivepassages. However, three mutations were found, Ile to Leu at position57, Gln to His at position 95, and Gln to stop at position 499 in theamino acid sequences of VSVG Although wild-type VSV G protein has 29residues of cytoplasmic domain, the last 13 residues of this domain weredeleted due to the Gln-to-stop mutation at position 499.

Biological properties of VSVG(HA)GFP(NA) virus. To determine whether VSVG protein is indeed incorporated into virions composed of otherinfluenza viral proteins, Western blot analysis was conducted onconcentrated VSVG(HA)GFP(NA) and WSN (control) viruses. As shown in FIG.20, VSV G protein, but not HA, was detected in VSVG(HA)GFP(NA) virions,confirming virion incorporation of VSV G protein.

Next, the growth properties of VSVG(HA)GFP(NA) virus were examined inBHK, CHO, or MDCK cells. Cells were infected at an MOI of 0.001, andyields of virus in the culture supernatant were determined at differenttimes post-infection at 37° C. by plaque assay on MDCK cells. Althoughlower than that of WSN virus, the maximum titer of VSVG(HA)GFP(NA) virusin both BHK and MDCK cells reached at least 10⁶ PFU per ml (FIG. 21). Incontrast to the poor growth of WSN virus in CHO cells, VSVG(HA)GFP(NA)virus grew as well in these cells as in the other two cell lines tested(FIG. 21). Moreover, during replication in each of the cell lines, cellsinfected with VSVG(HA)GFP(NA) virus expressed GFP.

These results indicated that both the HA(9)VSVG(80) andNA(183)GFP(157)Met(−) segments were efficiently incorporated intoinfluenza virions and that two foreign genes could be stably maintainedin influenza A virus during repeated passage.

Discussion

Determination of the genome packaging mechanisms is critical forunderstanding the life cycle of influenza virus as well as fordevelopment of influenza virus-based vectors for the expression offoreign proteins. In this study, it was demonstrated that sequences inboth the 3′ and 5′ ends of the coding regions in the HA vRNA wererequired for efficient incorporation of this segment into virions.Moreover, using this knowledge, a novel influenza-based virus wasgenerated that possesses two recombinant RNA segments containing thecoding sequences of VSV G and GFP flanked by sequences necessary forvirion incorporation of HA vRNA and NA vRNA, respectively, demonstratingstable expression of two foreign genes.

Several approaches have been reported for the development of vaccinevectors based on influenza A virus for expression of genes or portionsof genes from unrelated infectious agents. Short polypeptides have beeninserted into the antigenic sites of HA, resulting in positive immuneresponses against the inserted peptides. For the expression of longerpolypeptides and proteins, the foreign genes have been inserted into oneof the influenza virus genes, in which the foreign proteins wereexpressed by utilizing internal ribosomal entry sites (IRES) or thefoot-and-mouth disease virus 2A protease. Here, a new system wasestablished for the expression of a foreign protein, exploitingcis-acting virion incorporation signals in the NA and HA vRNAs. Thissystem enabled influenza-based virus to incorporate more than 1.5 kb ofa foreign gene (e.g., VSV G), demonstrating the potential of this vectorsystem. As the vaccine efficacy of replication-incompetent influenzaVLPs in mice has been shown, replication-incompetent influenza-basedVLPs with a recombinant RNA segment containing a gene from an unrelatedpathogen may serve as a promising vaccine. This potential is especiallyappealing for vaccination against HIV, foot-and-mouth disease and otherinfections, where any reversion of live vaccine viruses to wild-type isabsolutely unacceptable or where the efficacy of inactivated vaccinesmay be limited due to limited induction of mucosal immunity andcytotoxic T-lymphocyte responses. Thus, using this approach, aninfluenza virus can be employed as a vaccine vector. For example, onecan make a virus that contains a HIV gp160 coding region instead of HAand a gag coding region instead of NA (FIGS. 24 and 25). Moreover, ifVSV G replaces HA, M2 is no longer required and so three viral genes maybe replaced with heterologous genes. For instance, HA may be replacedwith HIV gp160, NA with gag and M2 with nef. The resulting recombinantinfluenza virus may be employed as a vaccine or as a booster for anotherHIV vaccine, e.g., a HIV DNA vaccine, to enhance or induce immunityincluding mucosal immunity. Alternatively, a vaccine may be amultivalent vaccine based on a recombinant influenza virus in which theNA coding segment is replaced with that of another pathogen, e.g.,glycoprotein D of herpes virus, which vaccine may result in a protectiveimmune response to influenza virus and herpes virus infections.

Viral vectors derived from adenoviruses, retroviruses, and poxvirusesefficiently introduce foreign genes into target cells. Since theseviruses contain DNA, or have DNA replication intermediates that could beintegrated into the host chromosome, the risk of adverse outcomes cannotbe eliminated. By contrast, such integration is improbable in influenzaviruses due to the lack of a DNA phase in infected cells. Moreover,since VSVG(HA)GFP(NA) virus does not require trypsin for HA cleavage,unlike typical influenza viruses, it may present a wider use. Inaddition, recombinant virus with desired cell tropism can be generatedby altering a glycoprotein on the virion surface. Thus, the systemutilizing cis-acting signals in vRNA segments for virion incorporationallows the design of recombinant influenza-based virus vectors that candeliver multiple foreign genes into target cells.

The assembly and release of viruses from epithelial cells is polarizedin some viruses, occurring selectively at either the apical orbasolateral surface. Polarized virus budding is thought to play a rolein determining the pathogenesis of viral infections. Influenza A virusbuds apically from infected epithelial cells and individually expressedHA, NA, and M2 proteins are also targeted to the apical surface of thecells. On the other hand, VSV is released from the basolateral surfaceof infected cells and VSV G protein is transported to the basolateralsurface. In the present study, a recombinant VSVG(HA)GFP(NA) virus,possessing VSV G, instead of the HA and NA proteins, was successfullygenerated. However, the VSV G protein of this recombinant virus lackedthe last 13 residues of the cytoplasmic domain due to a point mutation.Deletion of these 13 residues in the cytoplasmic domain is known toyield a protein that is more efficiently transported to the apicalsurface than the basolateral surface. Therefore, the mutation introducedinto the VSV G protein in VSVG(HA)GFP(NA) virus likely promoted itsefficient transport to the apical surface, leading to efficient buddingof VSVG(HA)GFP(NA) virus.

Influenza pandemics usually occur when a virus whose HA and/or NA areimmunologically distinct from those of the previous circulating strainappears upon reassortment of influenza viral RNA segments. Sequences inthe 3′ and 5′ ends of the coding regions within HA, NA, M, and NS vRNAsare required for their efficient incorporation into virions. Thepackaging of vRNA segments (most likely as a viral ribonucleoproteincomplex) is mediated by RNA-RNA interactions occurring in trans betweenthe viral RNA segments. If so, specific incorporation signals withineach segment may restrict reassortment of RNA segments. Empirically, itis known that influenza viral RNA segments do not reassort randomly.Functional interactions among proteins (e.g., formation of thepolymerase complex, HA-NA and cleavable HA-M2 functional associations)are thought to restrict random reassortment. In addition to theserestrictions on reassortment at the protein level, a similar restrictionmay exist at the RNA level. In this context, it is interesting that inboth the 1957 and 1968 pandemics, PB1 gene in addition to HA and/or NAgenes were introduced into human viruses from avian viruses, suggestinga possible link between the HA and PB1 RNA segments. Furthercharacterization of critical regions for virion incorporation of otherRNA segments may provide a clue to understanding reassortment of RNAsegments, leading to the prediction of the emergence of new pandemicstrains of influenza A virus.

In summary, with the information on the vRNA packaging signals, novelinfluenza vaccines and influenza-based vaccine vectors can be developed.

EXAMPLE 6

As illustrated in FIG. 26, a cell line that constitutively expresses aninfluenza virus-like RNA encoding a protein, e.g., NS2, can be made,although this RNA lacks an incorporation signal. A virus which lacks theNS2 coding sequence (NS2 KO) may also be prepared (Neumann et al., 2000;Watanabe et al., 2002). When NS2 KO virus infects normal cells, progenyvirus will not be produced, since the virus lacks NS2. In contrast, whenNS2 KO virus infects cells expressing an influenza virus-like RNAencoding NS2 but lacking an incorporation signal, NS2 is expressed uponviral infection and progeny NS2 KO virus is produced. However, theinfluenza virus-like RNA encoding NS2 will not be incorporated into NS2KO virus because it lacks a virion incorporation signal. Thus, NS2 KOremains replication-incompetent in normal cells. This system can be usedfor production of producer cells for replication-incompetent viruses.Using this system, producer cells expressing viral proteins, whosetoxicity to cells would typically prohibit generation of cell linesconstitutively expressing them, can be made. Thus, in this application,the knowledge of virion incorporation signals can be employed to designa system that does not allow a specific segment to be incorporated intovirions.

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All publications, patents and patent applications are incorporatedherein by reference. While in the foregoing specification this inventionhas been described in relation to certain preferred embodiments thereof,and many details have been set forth for purposes of illustration, itwill be apparent to those skilled in the art that the invention issusceptible to additional embodiments and that certain of the detailsdescribed herein may be varied considerably without departing from thebasic principles of the invention.

1. An influenza viral vector, comprising influenza virus incorporationsequences, which vector comprises: sequences corresponding to the 3′noncoding region of influenza virus HA vRNA, a heterologous nucleic acidsegment, 5′ HA incorporation sequences, and the 5′ noncoding region ofHA vRNA; wherein vRNA corresponding to the vector, when present in acell expressing influenza virus proteins and comprising vRNAs other thanthe vRNA corresponding to the vector, is packaged into virions. 2-5.(canceled)
 6. The vector of claim 1 wherein the 5′ HA incorporationsequences include at least 80 nucleotides corresponding to the 80 3′coding nucleotides of HA.
 7. The vector of claim 1 wherein the 5′ HAincorporation sequences include at least 291 nucleotides correspondingto the 291 3′ coding nucleotides of HA.
 8. The vector of claim 1 furthercomprising 3′ HA incorporation sequences.
 9. The vector of claim 8wherein the 3′ HA incorporation sequences include at least 3 nucleotidescorresponding to the first 3 coding nucleotides for HA.
 10. The vectorof claim 8 wherein the 3′ HA incorporation sequences include at least 9nucleotides corresponding to the first 9 coding nucleotides for HA. 11.The vector of claim 1 wherein the heterologous nucleic acid segmentcomprises sequences corresponding to an internal ribosome entrysequence.
 12. The vector of claim 1 wherein the heterologous nucleicacid segment comprises sequences corresponding to an open reading framefor a marker gene.
 13. The vector of claim 1 wherein the heterologousnucleic acid segment comprises sequences corresponding to an openreading frame for an immunogenic protein or a peptide of a pathogen, ora therapeutic protein.
 14. The vector of claim 1 wherein incorporationsequences are from a type A influenza virus.
 15. The vector of claim 1wherein the incorporation sequences are from a type B influenza virus.16. The vector of claim 1 wherein the heterologous nucleic acid segmentis fused to another nucleic acid segment so as to encode a fusionprotein.
 17. A recombinant influenza virus comprising a vRNAcorresponding to the vector of claim
 1. 18. The recombinant virus ofclaim 17 wherein the heterologous nucleic acid segment comprisessequences corresponding to an open reading frame for a marker gene. 19.The recombinant virus of claim 17 wherein the heterologous nucleic acidsegment comprises sequences corresponding to an open reading frame foran immunogenic protein or peptide of a pathogen.
 20. The recombinantvirus of claim 19 wherein the open reading frame encodes a HA protein.21. The recombinant virus of claim 19 wherein the open reading frameencodes a NA protein.
 22. The recombinant virus of claim 17 wherein theheterologous nucleic acid segment comprises sequences corresponding toan open reading frame for a transmembrane protein.
 23. The recombinantvirus of claim 17 wherein the heterologous nucleic acid segmentcomprises sequences corresponding to an open reading frame for a proteinwith membrane fusing activity.
 24. The recombinant virus of claim 17wherein the heterologous nucleic acid segment comprises sequencescorresponding to an open reading frame for a viral capsid protein. 25.The recombinant virus of claim 17 wherein the heterologous nucleic acidsegment comprises sequences corresponding to an open reading frame forvesicular stomatitis virus G protein.
 26. The recombinant virus of claim17 wherein the heterologous nucleic acid segment comprises sequencescorresponding to an open reading frame for a therapeutic protein. 27.The recombinant virus of claim 20 wherein the HA protein is a type B HAprotein.
 28. A method to express a heterologous nucleic acid segment ina cell, comprising: contacting a cell with the recombinant virus ofclaim 17 and detecting or determining whether a product encoded by theheterologous nucleic acid segment is expressed in the cell. 29-30.(canceled)
 31. An isolated nucleic acid molecule comprising influenzavirus HA incorporation sequences corresponding to the 3′ coding regionof HA and a heterologous nucleic acid segment. 32-33. (canceled)
 34. Thevector of claim 1 wherein vRNA corresponding to the vector, when presentin the cell, is packaged into virions at an efficiency at least 10% thatof a corresponding wild-type vRNA.
 35. The vector of claim 1 whereinvRNA corresponding to the vector, when present in the cell, is packagedinto virions at an efficiency at least 30% that of a correspondingwild-type vRNA.
 36. The vector of claim 1 wherein vRNA corresponding tothe vector, when present in the cell, is packaged into virions at anefficiency at least 60% that of a corresponding wild-type vRNA. 37-39.(canceled)